Re: [galaxy-user] Cuffdiff-cummerbund with biological replicates problem
In the past, others have had success using Cummerbund with Galaxy, and there's even a Cummerbund wrapper in the tool shed: http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund That said, it appears that replicate information is largely contained in the read group tracking files, which are not currently included in Galaxy's Cuffdiff outputs. I don't know if these files are required by Cummerbund to do replicate analysis. This would be a good question for the Cummerbund developers, as well as what the p and q values mean when doing replicate analysis. If you find that Galaxy's lacking something for Cummerbund to function correctly, that would be very useful information to share with the list. Best, J. On Jul 26, 2013, at 8:50 PM, Mike Shamblott wrote: I'm trying to run Cuffdiff on a set of 10 human samples with biological replication then download the results for further analyses in Cummerbund(v2.1.1). It seems like a standard workflow but I cannot get cummerbund to acknowledge replicates. I download and rename the 11 cuffdiff output files to the names expected by cummerbund. Cummerbund builds a CuffSet with no warnings and most analyses work as expected. The problem comes any time I try to see the results of replication. For example, in cummerbund, replicates() returns an empty set and any type of plot returns an error when replicates=T is included as an argument. There is no evidence of replication data in any of the 11 cuffdiff output files. The data is presented with the group name only. From this, I conclude that the problem is with cuffdiff, since there is no replicate data for cummerbund to build into its db. I see that there are several read group files that are produced by cuffdiff but cannot be downloaded in Galaxy. Is this the problem, and if so, how can Galaxy be used to generate data with (essential) replication? Are the p and q significance values reported in the output files a result of replicate analysis? I have tried to ask this question in several different forums without success. The responses I've gotten suggest its a Galaxy issue rather than either cuffdiff or cummerbund. I'm hoping someone here can help answer my questions. Hopeful, Mike ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] August 2013 Galaxy Update Newsletter is out
Hello all, The August 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08 . *Highlights:* - *GCC2013 Reporthttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#GCC2013_Report :* Meeting summaries, and links to videos, talks, posters, and Training Day materials. - Two new public servershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#New_Public_Servers - 47 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#New_Papers - SlipStream: Galaxy is now available as an appliancehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#SlipStream_Appliance:_Galaxy_Edition_Announced - There's a new Galaxy-Ptotoemics mailing listhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#New_Galaxy_Proteomics_Mailing_List - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#Who.27s_Hiring at eight different organizations - Galaxy @ ISMBhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#ISMB_.2F_ECCB_.2F_BOSC_.2F_MS_SIG_2013: links to slides and posters - Other Upcoming Eventshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#Other_Upcoming_Events including training in California, Sydney, Italy, Toulouse, and Boston. - New CloudMan Releasehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#CloudMan_Release - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#Other_News If you have anything you would like to see in the next *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Dave Clements and the Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Bowtie: Outputting unmapped reads
That's a neat trick, and I definitely wouldn't have thought of that approach, so thanks for that! After I finished writing this out, I realized it was super long. So here are the questions I'm asking up front, so you can choose whether or not to read the details. Thanks! 1. How do I output the quality scores when converting from FASTQ to FASTA? 2. Does the SAM-to-interval tool output only mapped reads by looking at the flag values? 3. Why am I getting the mentioned error and is there a way to resolve it? Here are the details: 1. I don't see an option to output both the sequences and the quality scores. I found two FASTQ-to-FASTA converters (one under the Convert Formats and the other in the FastX Toolkit) and both only output one fasta file with the sequences. Am I missing something, or should I be using some other tool to output both the sequences and the quality scores? 2. The Extract Genomic Sequences tool seems to want an Interval file as input, not a list of IDs. Does that mean I should convert the filtered SAM output to Interval? Currently I'm using the SAM-to-interval conversion to extract the mapped reads and make the data more manageable in one step (pretty sure I picked that up from one of the tutorials...). I was assuming that by definition it could only output an interval if it was mapped, and if so, I wouldn't be able to convert the unmapped reads to Interval anyway. Is that wrong? 3. I was setting up a workflow with Bowtie and I noticed that the Workflow Editor does show options to output unmapped reads. But when I try to output them, I get this error: Error due to input mapping of 'Compute quality statistics' in 'output_unmapped_reads_l'. A common cause of this is conditional outputs that cannot be determined until runtime, please review your workflow. Superficially, this seems silly. Obviously a conditional output will not be determined until runtime because it's dependent on something else. So why is that an error? I have tried outputting to a few different tools, so it doesn't seem to be specific to the tool into which the unmapped reads go (in this case, Compute Quality Statistics). Any thoughts, insights, or even other approaches to the original problem would be great. Currently, I'm thinking my best bet is to filter out the unmapped reads locally with a Perl script and re-upload, but that felt like overkill and time-consuming when I will inevitably want to tweak or re-run things. Also, installing a local instance is currently not an option for me (though it should be in a few months). In any case, I appreciate your help a lot! Thanks, again! Mayank Tandon On Thu, Jul 18, 2013 at 5:38 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Mayank, The best option I know of is to do the following: 1 - obtain the sequence identifiers for the unmapped reads by filter the SAM file, then cutting them out 2 - convert the original FASTQ file to FASTA - you should get two output, one for the sequences and one for the quality score values 3 - use the tool Fetch Sequences - Extract Genomic DNA. The query is the list from #1, the target is the genome from #2. Do this twice - once for seqs, once for quals. This means using the target datasets from #2 as Custom Reference genomes - help about how to do this is here: http://wiki.galaxyproject.org/Support#Custom_reference_genome 4 - combine the FASTA seq and qual files back to FASTQ If you will be doing this again, then capture the process into a workflow for future use, in a way creating your own tool. Hopefully this helps! Jen Galaxy On 7/18/13 9:40 AM, Mayank Tandon wrote: I was hoping this question had been asked, but I haven't been able to find it. I want to output the unmapped reads from bowtie as a fastq file for subsequent mapping to other genomes (i.e. the --un filename option). I know I can extract the unmapped reads by filtering on the bitwise values in the sam output and converting to fastq with the Picard tool, but I'm using colorspace data and bowtie converts them to letterspace. My understanding (coming mostly from forums and personal discussions) was that the color-to-letter conversion was somehow lossy so mapping the colorspace data directly is always preferable. So the question is: Is bowtie's '--un' option implemented in Galaxy and if so, how do I access it? Thanks in advance! Mayank Tandon ___ 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:
Re: [galaxy-user] Bowtie: Outputting unmapped reads
On Wednesday, July 31, 2013, Mayank Tandon wrote: That's a neat trick, and I definitely wouldn't have thought of that approach, so thanks for that! After I finished writing this out, I realized it was super long. So here are the questions I'm asking up front, so you can choose whether or not to read the details. Thanks! 1. How do I output the quality scores when converting from FASTQ to FASTA? You can't, unless you mean converting a FASTQ file into a FASTA and matching QUAL file? 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Bowtie: Outputting unmapped reads
Exactly. Jennifer's solution for outputting unmapped reads involves splitting the FASTQ file into basically two FASTA files, one with sequences and the other with the corresponding quality score string. So, yes, they would be matched files. On Wed, Jul 31, 2013 at 4:42 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wednesday, July 31, 2013, Mayank Tandon wrote: That's a neat trick, and I definitely wouldn't have thought of that approach, so thanks for that! After I finished writing this out, I realized it was super long. So here are the questions I'm asking up front, so you can choose whether or not to read the details. Thanks! 1. How do I output the quality scores when converting from FASTQ to FASTA? You can't, unless you mean converting a FASTQ file into a FASTA and matching QUAL file? 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
