Re: [galaxy-user] Patch for better FASTQ description handling
On Wed, Oct 19, 2011 at 4:53 AM, Florent Angly florent.an...@gmail.com wrote: I have had the chance to try the patch on several datasets and it looks good :) I reiterate my suggestion to pull the patch in galaxy-central. Best, Florent It looks sensible, although I would add a comment to the join method to say the description from read1 is taken (if the reads differ in their descriptions). Mind you, the whole module seems to lack docstrings ;) Are there any unit tests (not that Galaxy seems to insist on them)? 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] Patch for better FASTQ description handling
Hi Florent, Sorry for the delay. I did try the patch out shortly after you contributed it, but it caused the functional to fail. I was able to fix the issue and allow the existing tests to start passing, but I've been bogged down lately and haven't been able to perform a more thorough review of the code. If you could provide tests with files (e.g. for the tools affected) that test the new functionality, that would be a great help. The use of partition removes python compatibility for 2.5, although this is a lesser/non-concern. Also, I'm not entirely sold on having the Identifier line being parsed as identifier + space + description instead a single identifier line. This would mean that identifiers could not themselves contain spaces, but There is no standardization for identifiers (so they could technically have spaces?). Could two different reads be identified as Read A and Read B, but then would no longer be uniquely identifiable as each would then be identified as Read. If this added functionalilty were introduced as optional behavior (e.g. a user needs to click a checkbox on the tools to apply the id line splitting), these concerns can be mitigated. Peter, Florent, anyone else: I'd be very interested to hear your thoughts on the above, particularly in respect to know real-world data. For now, lets discount SRA data from this discussion. Thanks, Dan On Oct 19, 2011, at 5:00 AM, Peter Cock wrote: On Wed, Oct 19, 2011 at 4:53 AM, Florent Angly florent.an...@gmail.com wrote: I have had the chance to try the patch on several datasets and it looks good :) I reiterate my suggestion to pull the patch in galaxy-central. Best, Florent It looks sensible, although I would add a comment to the join method to say the description from read1 is taken (if the reads differ in their descriptions). Mind you, the whole module seems to lack docstrings ;) Are there any unit tests (not that Galaxy seems to insist on them)? 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/ ___ 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] Query regarding RNA-Seq data analysis
Hello, Use Get Data - Upload or load your data into Galaxy with FTP (if large): http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP Once the data is in Galaxy, this tutorial covers the general analysis path for RNA-seq data: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq Hopefully this helps to get you started, Best, Jen Galaxy team On 10/18/11 10:24 PM, santhi ramachandran wrote: Hi, I am having a fastq file for my RNA data analysis in my computer. How to make it available for RNA seq data analysis using tophat. Sandy ___ 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/
[galaxy-user] one error while installing galaxy
Hi, When I installed galaxy, one error message appeared, which said that ImportError: No module named distutils.util Fetch failed. Could you tell me how to solve this problem? Thank you very much! ___ 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] bed12 format for stitching blocks given a set of coding exon intervals
Hi Galaxy, I am trying to stitch together MAF alignments for the coding sequence for a few genes of interest in Drosophila. I used UCSC to send the bed intervals of the coding exons of my gene and sent the output to Galaxy. But when I try and use the tool Stitch Gene blocks it complains that my bed is a bed3 and not a bed12. I'm a bit rusty with my browser skills, but how can I send my output to Galaxy as a bed12 format so I can stitch my MAF blocks together? Thanks for your help! Amit -- Amit Indap ___ 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] Patch for better FASTQ description handling
Peter and Daniel, thanks for the comments. On 19/10/11 23:49, Peter Cock wrote: On Wed, Oct 19, 2011 at 2:31 PM, Daniel Blankenbergd...@bx.psu.edu wrote: Hi Florent, Sorry for the delay. I did try the patch out shortly after you contributed it, but it caused the functional to fail. I was able to fix the issue and allow the existing tests to start passing, but I've been bogged down lately and haven't been able to perform a more thorough review of the code. If you could provide tests with files (e.g. for the tools affected) that test the new functionality, that would be a great help. I'll have a look at that. The use of partition removes python compatibility for2.5, although this is a lesser/non-concern. I guess you could use split, but special case on there being no space. Also, I'm not entirely sold on having the Identifier line being parsed as identifier +space + description instead a single identifier line. That is the normal convention, just like with FASTA. http://dx.doi.org/10.1093/nar/gkp1137 The Bioperl and Biopython projects use this convention for FASTA and FASTQ files. This would mean that identifiers could not themselves contain spaces, but There is no standardization for identifiers (so they could technically have spaces?). Could two different reads be identified as Read A and Read B, but then would no longer be uniquely identifiable as each would then be identified as Read. If this added functionalilty were introduced as optional behavior (e.g. a user needs to click a checkbox on the tools to apply the id line splitting), these concerns can be mitigated. That is expected, @Read A and @Read B have the same identifier, Read. Peter, Florent, anyone else: I'd be very interested to hear your thoughts on the above, particularly in respect to know real-world data. For now, lets discount SRA data from this discussion. See also the new Illumina 1.8 naming convention where they dropped the /1 and /2 and hit it in the description. It should be tested, but I think Florent's patch will work here (while the current Galaxy behaviour won't). Peter I was not aware of this new naming. It seems like a terrible decision from Illumina because now both reads in a pair technically have the same ID (but a different description). Florent ___ 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/
