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
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.
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.
Second, for some reason, the Illumina fastq files will not load on the web version or my local version either.
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.
Hi,
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.
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.
Second, for some reason, the Illumina fastq files will not load on the web version or my local version either.
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.)
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
On Jan 28, 2011, at 2:38 AM, Steve Taylor wrote:
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.) 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)?
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
participants (4)
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Dannon Baker -
Jeremy Goecks -
Shawn Starkenburg -
Steve Taylor