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Question: Fastq And Index File Upload Problems
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gravatar for Shawn Starkenburg
7.8 years ago by
Shawn Starkenburg • 10
Shawn Starkenburg • 10 wrote:
I'm trying to create a RNA-Seq Workflow with Bowtie/Tophat and Cufflinks using a newly assembled genome (not public). I created the genome index files via Bowtie locally but Galaxy will not accept the .ebwt index files (n=4)--"Inappropriate content" error. Second, for some reason, the Illumina fastq files will not load on the web version or my local version either. (FYI, I successfully ran these same files through our local command line version of Tophat and Cufflinks without problems) Please advise. Thanks, Shawn
rna-seq alignment bowtie cufflinks • 1.0k views
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modified 7.8 years ago by Jeremy Goecks • 2.2k • written 7.8 years ago by Shawn Starkenburg • 10
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gravatar for Jeremy Goecks
7.8 years ago by
Jeremy Goecks • 2.2k
Jeremy Goecks • 2.2k wrote:
Galaxy will not accept Bowtie indices. When you provide Bowtie/Tophat with a custom genome via Galaxy, Galaxy will create the indices needed for the tool to run before running the tool. You'll need to groom the files to convert them from fastq format to fastqsanger format, which is the format accepted by Galaxy's NGS tools. See the FastqGroomer tool for details. (If you're confident your fastq quality scores are in Sanger format, you can simply change the fastq dataset's datatype by clicking on its pencil and looking for the datatype selection on the page. This will take less time than running the groomer.) Thanks, J.
ADD COMMENT • link written 7.8 years ago by Jeremy Goecks • 2.2k
Hi, Assuming you are confident of the fastq format, is there anyway to do this non-interactively, so you can run bowtie directly on the fastq sequences without using FastqGroomer (for example, in a Workflow)? Thanks, Steve
ADD REPLY • link written 7.8 years ago by Steve Taylor • 240
One option for handling this within workflows is to add a "Change Datatype" action to the previous step with the fastq file, and set it to fastqsanger that way. This doesn't manipulate the dataset at all or try to do any conversion, it just changes the datatype. -Dannon
ADD REPLY • link written 7.8 years ago by Dannon Baker ♦ 3.7k
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