Re: [galaxy-user] Megablast database identity
Hello, The Megablast htgs, nt, and wgs databases are in the process of being updated to the latest NCBI releases and are expected to be available by tomorrow morning (possibly sooner). Should you wish to continue your analysis using the prior versions, these are available through our rsync server for use in a local production or cloud Galaxy. https://wiki.galaxyproject.org/Admin/UseGalaxyRsync http://getgalaxy.org http://usegalaxy.org/cloud Also posted to Galaxy Biostar: https://biostar.usegalaxy.org/p/7335/#7340 Best, Jen Galaxy team On 4/27/14 4:25 AM, Scott W. Tighe wrote: Jennifer I am megablasting a simple 500,000 line dataset that is certainly in galaxy fasta. For a week i have been seeing numerous errors. So i have reprocesed the data multiple times. The error message is could not find specified database directory Is there an alternative approach? I did try ncbi directly and that failed too. They say they have a database issue Scott Tighe Core Laboratory Research Staff Advanced Genome Technologies Core Deep Sequencing (MPS) Facility Vermont Cancer Center 149 Beaumont Ave University of Vermont HSRF 303 Burlington Vermont USA 05045 802-656-AGTC 802-999- (cell) ___ The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/ Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/ Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Megablast database identity
Jennifer I am megablasting a simple 500,000 line dataset that is certainly in galaxy fasta. For a week i have been seeing numerous errors. So i have reprocesed the data multiple times. The error message is could not find specified database directory Is there an alternative approach? I did try ncbi directly and that failed too. They say they have a database issue Scott Tighe Core Laboratory Research Staff Advanced Genome Technologies Core Deep Sequencing (MPS) Facility Vermont Cancer Center 149 Beaumont Ave University of Vermont HSRF 303 Burlington Vermont USA 05045 802-656-AGTC 802-999- (cell) ___ The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/ Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] MegaBLAST output
Dear all, Sometimes ago, I’ve reported on this list the same problem with megablast than Sarah mentioned. I finally used another way to analyse my data but my conclusion was similar to Sarah one with most of the time a shift of « -1 » between the GI number in the output and the following parameters in the other columns. One of the possible explanations was maybe a change in the GI number according to the version of the databank used. However, I’m not so sure that this explanation is the right one and I’m not so sure about the consistency of this « GI-1 » rule. Indeed, I’ve made a simple test by using a known and well identified sequence taken at random in Genbank (GI 2924630 in NCBI, AB002412.1, Elephas maximus mitochondrial DNA for cytochrome b, 1137 bp, so called TEST-SEQ below). Using this sequence as template for megablast in Galaxy gave the following results (3 first lines): TEST-SEQ 2924736 1137 100.00 1137 0 0 1 1137 1 1137 0.0 2254.0 TEST-SEQ 155573765 16831 99.91 1137 1 0 1 1137 14149 15285 0.0 2246.0 TEST-SEQ 2924608 1137 99.74 1137 3 0 1 1137 1 1137 0.0 2230.0 As you can see, the parameters concerning the first match seem correct : 1137 bp and 100% of identity. However, the GI number is not the good one (2924736 instead of 2924630) and we don’t have a « GI-1 » rule here. I used the Fetch Taxonomic Representation command available in Galaxy to fetch the taxonomy for the 3 sequences above and 2 out 3 GI numbers correspond to very distant taxa… I did a megablast on the NCBI (so, the database is more recent) to compare and here are the results : TEST-SEQ gi|2924630|dbj|AB002412.1| 100.00 1137 0 0 1 1137 1 1137 0.0 2100 TEST-SEQ gi|37496447|emb|AJ428946.1| 99.91 1137 1 0 1 1137 14149 15285 0.0 2095 TEST-SEQ gi|2924606|dbj|D50844.1| 99.74 1137 3 0 1 1137 1 1137 0.0 2084 At this step, I would say that the table given in output of the megablast in Galaxy is good for all parameters except for the GI of the database hit (column 2)…and I'm not able to say why. I’m not sure that it can help… Hoping that you will be able to clarify this possible problem in the megablast output, Best, Sandrine 2012/4/24 Sarah Hicks garlicsc...@gmail.com: So, Jen, I'm not sure if we're talking about the same ID change... I am under the impression that GenBank does not change it's GI numbers for it's entries. Plus, it's now looking like all sequence length output info for each hit through Galaxy's megablast does not match to the GI number output given by Galaxy megablast, but to the GI number before it. Because the -1 rule is so consistent, it makes this seem less and less like it has to do with NCBI changing it's GI numbers to make room for new entries or something. In other words, there is a shift, as if a 1 was added to each NCBI GI number in galaxy before galaxy produces the output file. I need someone to tell me if I can trust the output. Basically I see it this way. Every hit row from Galaxy megablast actually has information for two NCBI entries: the one that shares the GI output and the one before it that shares the sequence length output. Which one is the hit I should be using? Because on some occations, the NCBI entry that shares the GI output from galaxy is VERY distantly related to the NCBI entry that shares the subject sequence length output from galaxy, and I don't know which to pick. Is this problem well understood, yet? On Tue, Apr 24, 2012 at 10:52 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Apr 23, 2012 at 11:41 PM, Sarah Hicks garlicsc...@gmail.com wrote: Peter, you requested an example, here are the first five hits for my first query sequence (OTU#0) 0 324034994 527 93.23 266 13 5 1 265 22 283 7e-102 379.0 0 56181650 513 93.26 267 10 8 1 265 25 285 7e-102 379.0 0 314913953 582 91.79 268 13 9 1 265 24 285 2e-92 347.0 0 305670062 281 92.52 254 14 5 4 256 32 281 2e-92 347.0 0 310814066 1180 91.73 266 14 7 1 265 24 282 9e-92 345.0 You will notice there are 13 columns, one in addition to the 12 column titles you explained. This is because there is a column between sseqID and pident. I see now - the megablast_wrapper.py calls megablast (from the old legacy NCBI blast suite) which does indeed produce 12 column tabular output. But the wrapper script then edits the output: It appears to be splitting column 2 in two at the underscore intended to give the match ID and the length. This puzzles me but I haven't used the legacy BLAST tabular output for a while. On BLAST+ you can ask for the query or subject length explicitly as their own columns so we don't have this problem. The megablast_wrapper.py also re-formats the floating point score in the last column, apparently the
Re: [galaxy-user] MegaBLAST output
Hi Sarah, We appreciate all of the information you have provided and have been working here since yesterday to investigate the issue in more detail. This includes incorporating the additional data both you and Peter have been posting. We don't have anything conclusive to report yet, but it would have been considerate to send an update this morning to let you know what we were doing. Please accept my apologies for not doing so - we are in fact in complete agreement that as the data currently presents, something odd appears to be going on. Genbank updates would be unrelated as gi numbers do not change through time (although they can be retired, but again, not related to this case). The question of the mismatch in the wrapped Megablast output between gi and reported length is the open issue to be addressed. A reply will be send as soon as the root cause is determined. If there is indeed a problem, this would of course be considered a priority to correct. Not that we are expecting delays, but if your analysis is very urgent, using the BLAST+ BLASTN megablast wrapper that Peter authored, in a local or cloud instance, would be the best immediate remedy (this version has the standard 12 column output). Sequence length data could always be obtained from Genbank and added into these results using other Galaxy tools (column join, etc.). Thank you and Peter both for the help and for your patience! Best, Jen Galaxy team On 4/24/12 1:50 PM, Sarah Hicks wrote: So, Jen, I'm not sure if we're talking about the same ID change... I am under the impression that GenBank does not change it's GI numbers for it's entries. Plus, it's now looking like all sequence length output info for each hit through Galaxy's megablast does not match to the GI number output given by Galaxy megablast, but to the GI number before it. Because the -1 rule is so consistent, it makes this seem less and less like it has to do with NCBI changing it's GI numbers to make room for new entries or something. In other words, there is a shift, as if a 1 was added to each NCBI GI number in galaxy before galaxy produces the output file. I need someone to tell me if I can trust the output. Basically I see it this way. Every hit row from Galaxy megablast actually has information for two NCBI entries: the one that shares the GI output and the one before it that shares the sequence length output. Which one is the hit I should be using? Because on some occations, the NCBI entry that shares the GI output from galaxy is VERY distantly related to the NCBI entry that shares the subject sequence length output from galaxy, and I don't know which to pick. Is this problem well understood, yet? On Tue, Apr 24, 2012 at 10:52 AM, Peter Cockp.j.a.c...@googlemail.com wrote: On Mon, Apr 23, 2012 at 11:41 PM, Sarah Hicksgarlicsc...@gmail.com wrote: Peter, you requested an example, here are the first five hits for my first query sequence (OTU#0) 0 324034994 527 93.23 266 13 5 1 265 22 283 7e-102 379.0 0 56181650513 93.26 267 10 8 1 265 25 285 7e-102 379.0 0 314913953 582 91.79 268 13 9 1 265 24 285 2e-92 347.0 0 305670062 281 92.52 254 14 5 4 256 32 281 2e-92 347.0 0 310814066 118091.73 266 14 7 1 265 24 282 9e-92 345.0 You will notice there are 13 columns, one in addition to the 12 column titles you explained. This is because there is a column between sseqID and pident. I see now - the megablast_wrapper.py calls megablast (from the old legacy NCBI blast suite) which does indeed produce 12 column tabular output. But the wrapper script then edits the output: It appears to be splitting column 2 in two at the underscore intended to give the match ID and the length. This puzzles me but I haven't used the legacy BLAST tabular output for a while. On BLAST+ you can ask for the query or subject length explicitly as their own columns so we don't have this problem. The megablast_wrapper.py also re-formats the floating point score in the last column, apparently the NCBI style could cause problems with the Galaxy filter tool. In the metagenomic tutorial the first 4 columns are explained, and column 3 is described as length of sequence in database (or length of the subject sequence). This is the problem column. The length of only one of the subject GI numbers above match the subject length in NCBI. This has caused me to wonder if I can trust the hit info. In all cases that I've checked, when this happens the correct match is the listed GI value minus 1 (ie, in NCBI, gi|324034994 is not 527nt long, but 324034993 IS 527nt long). That is strange. Peter -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User
Re: [galaxy-user] MegaBLAST output
On Tue, Apr 24, 2012 at 10:24 PM, Jennifer Jackson j...@bx.psu.edu wrote: ..., using the BLAST+ BLASTN megablast wrapper that Peter authored, in a local or cloud instance, would be the best immediate remedy (this version has the standard 12 column output). Sequence length data could always be obtained from Genbank and added into these results using other Galaxy tools (column join, etc.). Getting the query and match sequence lengths is even simpler that that with the BLAST+ wrappers - just select the extended tabular output. Of course, you'll need to adjust the downstream analysis to take into account the different column numbers. Peter ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] MegaBLAST output
Thanks Peter, Excellent point. From there, the Cut tool could be used to reorganize the output to exactly match that of the 13-column regular megablast output. So, no external data needed, no tool modifications needed. This can't be done on the main public Galaxy instance as BLAST+ is not available there, but for any local/cloud instance this is an alternative certainly work testing. Best, Jen Galaxy team On 4/24/12 2:36 PM, Peter Cock wrote: On Tue, Apr 24, 2012 at 10:24 PM, Jennifer Jacksonj...@bx.psu.edu wrote: ..., using the BLAST+ BLASTN megablast wrapper that Peter authored, in a local or cloud instance, would be the best immediate remedy (this version has the standard 12 column output). Sequence length data could always be obtained from Genbank and added into these results using other Galaxy tools (column join, etc.). Getting the query and match sequence lengths is even simpler that that with the BLAST+ wrappers - just select the extended tabular output. Of course, you'll need to adjust the downstream analysis to take into account the different column numbers. Peter -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] MegaBLAST output
I am having trouble finding information on the MegaBLAST output columns. What is each column for? I can't seem to figure this out by comparing info in the columns to NCBI directly because the GI#'s don't match with the correct entry on NCBI. I've seen that others have posted about that problem, so I'm also waiting on details on that question, but for now, I'd just like to know what to make of the output... best, Sarah ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] MegaBLAST output
Hi Sarah, Peter defined the columns (thanks) but I can provide some information about the GenBank identifiers. The megablast database on the public server are roughly a year old and there have been updates at NCBI since that time. As I understand it, this manifests as occasional mismatches between hits at Galaxy vs Genbank when comparing certain IDs linked to updated records. We are working to update these three databases, but there are some complicating factors around this processing specifically related to the public instance and the metagenomics workflow that have yet to be resolved. Please know that getting updated is a priority for us and we apologize for the inconvenience. To use the most current databases, a local or (better) cloud instance with either the regular or BLAST+ version of the tool and a database your choice is the recommendation. Instructions to get started are at: getgalaxy.org getgalaxy.org/cloud Hopefully this explains the data mismatch. This question has come up before, but I think you are correct in that the final conclusion never was posted back to the galaxy-user list (for different reasons). So, thank you for asking so we that could send out a clear reply for everyone using the tool. Best, Jen Galaxy team On 4/23/12 9:56 AM, Sarah Hicks wrote: I am having trouble finding information on the MegaBLAST output columns. What is each column for? I can't seem to figure this out by comparing info in the columns to NCBI directly because the GI#'s don't match with the correct entry on NCBI. I've seen that others have posted about that problem, so I'm also waiting on details on that question, but for now, I'd just like to know what to make of the output... best, Sarah ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] MegaBLAST output
Thanks so much for the prompt reply. I don't mind using last years GenBank, as long as I am getting accurate hits. I just have a couple more questions to confirm I am safe using the Galaxy pipline for this... So if I continue to work within the the 1 year old database, can I trust the output as accurate matches? Specifics about my project: I have environmental samples that were sequenced for fungal ITS. I have clustered these into OTUs, and chosen a representative sequence for each. If I retrieve hits for this representative sequence file in my sample, can I trust the hits as being the correct hits as of last year? I'm just worried about what that one person said who thought there was some column arrangement problems, because I'm finding that I'm getting hits from different phylum for the same sequence using default parameters in megablast... Can I also assume, then, that I should NOT identify my representative sequence file to updated GI numbers using another pipeline, and then bring the file of GI numbers to Galaxy to fetch taxonomic assignments? (which I would do because of the nice neat columns for each taxonomic level Galaxy puts out) Sarah On Mon, Apr 23, 2012 at 2:26 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Sarah, Peter defined the columns (thanks) but I can provide some information about the GenBank identifiers. The megablast database on the public server are roughly a year old and there have been updates at NCBI since that time. As I understand it, this manifests as occasional mismatches between hits at Galaxy vs Genbank when comparing certain IDs linked to updated records. We are working to update these three databases, but there are some complicating factors around this processing specifically related to the public instance and the metagenomics workflow that have yet to be resolved. Please know that getting updated is a priority for us and we apologize for the inconvenience. To use the most current databases, a local or (better) cloud instance with either the regular or BLAST+ version of the tool and a database your choice is the recommendation. Instructions to get started are at: getgalaxy.org getgalaxy.org/cloud Hopefully this explains the data mismatch. This question has come up before, but I think you are correct in that the final conclusion never was posted back to the galaxy-user list (for different reasons). So, thank you for asking so we that could send out a clear reply for everyone using the tool. Best, Jen Galaxy team On 4/23/12 9:56 AM, Sarah Hicks wrote: I am having trouble finding information on the MegaBLAST output columns. What is each column for? I can't seem to figure this out by comparing info in the columns to NCBI directly because the GI#'s don't match with the correct entry on NCBI. I've seen that others have posted about that problem, so I'm also waiting on details on that question, but for now, I'd just like to know what to make of the output... best, Sarah ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] MegaBLAST output
Peter, you requested an example, here are the first five hits for my first query sequence (OTU#0) 0 324034994 527 93.23 266 13 5 1 265 22 283 7e-102 379.0 0 56181650513 93.26 267 10 8 1 265 25 285 7e-102 379.0 0 314913953 582 91.79 268 13 9 1 265 24 285 2e-92 347.0 0 305670062 281 92.52 254 14 5 4 256 32 281 2e-92 347.0 0 310814066 118091.73 266 14 7 1 265 24 282 9e-92 345.0 You will notice there are 13 columns, one in addition to the 12 column titles you explained. This is because there is a column between sseqID and pident. In the metagenomic tutorial the first 4 columns are explained, and column 3 is described as length of sequence in database (or length of the subject sequence). This is the problem column. The length of only one of the subject GI numbers above match the subject length in NCBI. This has caused me to wonder if I can trust the hit info. In all cases that I've checked, when this happens the correct match is the listed GI value minus 1 (ie, in NCBI, gi|324034994 is not 527nt long, but 324034993 IS 527nt long). On Mon, Apr 23, 2012 at 11:05 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Apr 23, 2012 at 5:56 PM, Sarah Hicks garlicsc...@gmail.com wrote: I am having trouble finding information on the MegaBLAST output columns. What is each column for? I can't seem to figure this out by comparing info in the columns to NCBI directly because the GI#'s don't match with the correct entry on NCBI. I've seen that others have posted about that problem, so I'm also waiting on details on that question, but for now, I'd just like to know what to make of the output... best, Sarah I've not tried to track down this reported possible bug in GI numbers, and weather it also affects BLAST+ as well as the legacy NCBI BLAST (which has now been discontinued). Do you have a specific example. As to the 12 columns, they are standard BLAST tabular output, and should match the defaults in BLAST+ tabular output which are: Column NCBI name Description 1 qseqid Query Seq-id (ID of your sequence) 2 sseqid Subject Seq-id (ID of the database hit) 3 pident Percentage of identical matches 4 length Alignment length 5 mismatch Number of mismatches 6 gapopen Number of gap openings 7 qstart Start of alignment in query 8 qend End of alignment in query 9 sstart Start of alignment in subject (database hit) 10 send End of alignment in subject (database hit) 11 evalue Expectation value (E-value) 12 bitscore Bit score Peter ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Megablast question
Hi Vasu, The three primary megablast databases available on the public main Galaxy instance are comprised of individual fragments/sequences of different types from many species (not assembled genomes): http://user.list.galaxyproject.org/Question-about-megablast-td4543260.html If you want to use megablast to map against specific assembled genomes, then using a local or (better) cloud instance is recommended. In your own instance, the individual genomes would be set up the way that the 'phiX174' is set up on main. To get started, please see: http://getgalaxy.org Does this address your question? If not, perhaps you could explain more what your goal is and we can try to offer help or confirm that this is the best path? Regards, Jen Galaxy team On 4/10/12 11:04 AM, shamsher jagat wrote: Hi, I am using megablast and was wondering how can I get chromosome number and coordinates of its hits. Thanks Shamesher ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Megablast question
Hi, I am using megablast and was wondering how can I get chromosome number and coordinates of its hits. Thanks Shamesher ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Megablast
Hello Scott, For #1, option -p: Here is a link to some megablast parameter documentation online: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/megablast.html#3 (the primary paper for the Galaxy tool is noted at the bottom of the tool form, but this is convenient) Quote: Table 3.30 Parameter -p FunctionSpecifies the percentage identity cut-off Default 0 Input format[Real] Example To set percent id cutoff to 75%, use: -p 75 Note: The input value range is between 0 and 100, with 0 meaning no cutoff. It only works on the aligned region or individual HSPs. For #2, there are a few ways to interpret filter. If you mean will megablast consider the adapter part of the sequence in calculations, the answer is that it does for some and doesn't for others. The part of the sequence that is adapter wouldn't align to the genome, and percent identity is only based on HSPs (high scoring pairs - one part of the pair is the DNA query and the other is the genome target, for that alignment region only). So, adapter sequence wouldn't be involved in percent identify calculations (or be expected to!). But, these unaligned regions could become a problem if coverage or certain other statistics were part of your analysis. Learning about the statistics you choose to use, to see if query length is part of the calculation, will let you know if clipping is necessary. If important, removing adapters can be done with tools in NGS: QC and manipulation (perform a tool search on keywords trim or clip. Best, Jen Galaxy team On 2/20/12 4:59 PM, Scott Tighe wrote: Hi Galaxy users When Magablasting 1)what does the identity value -p mean ...is it percent identity? I want my megablast results to be reported form only a 100% match. I do not see a place for % alinement concordance. 2) form my Illumina Hiseq reads, are the adaptor sequences filtered during the filter step? Scott tighe --2 Scott Tighe Advanced Genome Technology Lab Vermont Cancer Center at the University of Vermont 149 Beaumont Avenue Health Science Research Bd RM 305 Burlington Vermont USA 05405 lab 802-656-AGTC (2482) cell 802-999- ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Megablast question
Hi Scott I never used megablast so what i am writing is true of just any fasta file (so if there is anything quirky in megablast that i dont know about, apologies!): Take your fasta file and convert to tabular (under "fasta manipulation" - this will make it go to one line per record). Then randomly choose whatever number of reads you want using "select random lines from a file" under the text maniupulation tab. Then convert the tabular file back to fasta. (under the fasta manipulation tab) noa On 16/02/2012 19:31, Scott Tighe wrote: Hi all When using Galaxy megablast, is there a simple way to reduce my FASTA files from 23 million reads to 1/2 that size and submit to megablast separately? Thanks -- Scott Tighe Advanced Genome Technology Lab Vermont Cancer Center at the University of Vermont 149 Beaumont Avenue Health Science Research Bd RM 305 Burlington Vermont USA 05405 lab 802-656-AGTC (2482) cell 802-999- ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Megablast question
Noa has the right idea, but if you're asking for how to split a dataset into two non-overlapping halves you'll want to use Select First and Select Last, instead of random lines. Get an accurate line count from your file using the Line/Word/Character count tool and then split it right in the middle using select first/last. -Dannon On Feb 16, 2012, at 2:35 PM, Noa Sher wrote: Hi Scott I never used megablast so what i am writing is true of just any fasta file (so if there is anything quirky in megablast that i dont know about, apologies!): • Take your fasta file and convert to tabular (under fasta manipulation - this will make it go to one line per record). • Then randomly choose whatever number of reads you want using select random lines from a file under the text maniupulation tab. • Then convert the tabular file back to fasta. (under the fasta manipulation tab) noa On 16/02/2012 19:31, Scott Tighe wrote: Hi all When using Galaxy megablast, is there a simple way to reduce my FASTA files from 23 million reads to 1/2 that size and submit to megablast separately? Thanks -- Scott Tighe Advanced Genome Technology Lab Vermont Cancer Center at the University of Vermont 149 Beaumont Avenue Health Science Research Bd RM 305 Burlington Vermont USA 05405 lab 802-656-AGTC (2482) cell 802-999- ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
