Question: Re: Fastq Type Change
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gravatar for Jeremy Goecks
7.8 years ago by
Jeremy Goecks2.2k
Jeremy Goecks2.2k wrote:
Steve, I'm sending this question along to the galaxy-user list because it's likely of interest to others as well as yourself. Dannon, our resident workflow expert, should be able to answer your question. Thanks, J.
galaxy • 750 views
ADD COMMENTlink modified 7.8 years ago by Dannon Baker3.7k • written 7.8 years ago by Jeremy Goecks2.2k
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gravatar for Dannon Baker
7.8 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:
If you're confident about the format of the dataset in question, add a Change Datatype action to your workflow (on the step before bowtie) that sets the datatype to fastqsanger. See the right panel of the workflow editor under Step Actions; you want something like this:
ADD COMMENTlink written 7.8 years ago by Dannon Baker3.7k
Thanks. What if (after upload) this is your first step? With 'Upload' you don't get the option to do 'Change Datatype'. Steve
ADD REPLYlink written 7.8 years ago by Steve Taylor240
I'm not exactly sure I follow. If the first step in your workflow after the Input Dataset step is Bowtie, then you won't want to do this in the workflow, it should happen prior to that. The workflow expects that you're supplying the correct format for that first step. When you are first uploading the file you can specify at that time that it should be a fastqsanger file. For datasets that are already in a history, you can click the pencil icon on the history item and change the datatype there without running the fastq groomer. Let me know if I've misunderstood and this doesn't cover what you're looking to do. Thanks! -Dannon
ADD REPLYlink written 7.8 years ago by Dannon Baker3.7k
I think you have but it doesn't help. :-) The issue is we get a lot of Illumina 1.3+ format FASTQ files and bowtie in Galaxy by default doesn't accept them although there is an option on the command line bowtie to read these. So I think the solution seems to be either hardwire the code in our local Galaxy instance to use the --solexa1.3-quals option or (probably more useful) put a drop down list in the web UI to allow the user to set the format of the fastq sequences on the bowtie tool. Thanks for you help, Steve
ADD REPLYlink written 7.8 years ago by Steve Taylor240
On Thu, Feb 10, 2011 at 12:49 PM, Stephen Taylor Not the best approach. I think you should update the XML to include the --solexa1.3-quals option if the Galaxy file format is fastqillumina, see for example (in the reverse situation) the -Q 33 option is only used on fastqsanger when calling the FASTX tools, e.g. https://bitbucket.org/galaxy/galaxy- central/src/default/tools/fastx_toolkit/fastx_clipper.xml That way the user must mark their FASTQ file type as usual (at upload time or via the "pencil icon" to edit the attributes), and then bowtie will be called appropriately. Peter
ADD REPLYlink written 7.8 years ago by Peter Cock1.4k
Ok. Cool. I didn't realise you could do that! Sounds like this should be added into the main release. It would save a lot of time/disk space instead of using Groomer. Thanks, Steve
ADD REPLYlink written 7.8 years ago by Steve Taylor240
On Thu, Feb 10, 2011 at 6:34 PM, Stephen Taylor I agree. Maybe Dan can take care of it - I don't have bowtie setup on our local Galaxy (yet) so I wouldn't be able to test the proposed fix. In the long term however the Solexa/Illumina FASTQ formats are on their way out since CASAVA 1.8 will switch to the Sanger FASTQ encoding: http://seqanswers.com/forums/showthread.php?t=8895 Peter
ADD REPLYlink written 7.8 years ago by Peter Cock1.4k
Hi Stephen and Peter, This change is definitely possible, and because the SAM format specifies that its quality scores are phred scaled and ASCII offset of 33 (regardless of provided input) it shouldn't cause complications downstream. We'll add this to our todo list. I created a ticket: https://bitbucket.org/galaxy/galaxy-central/issue/471/allow-bowtie- mapper-to-accept-fastq that you can follow if you like. Thanks, Dan
ADD REPLYlink written 7.8 years ago by Daniel Blankenberg ♦♦ 1.7k
Hi Stephen, Maybe you should file an issue on bitbucket about extending the Bowtie wrapper to support fastqillumina as well as fastqsanger as input? https://bitbucket.org/galaxy/galaxy- central/issues?status=new&status=open The current version of the wrapper is here if you want to look at it: https://bitbucket.org/galaxy/galaxy- central/src/default/tools/sr_mapping/bowtie_wrapper.xml Peter
ADD REPLYlink written 7.8 years ago by Peter Cock1.4k
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