The indexing should be automatic. We'll need to look at it in more detail. -- jt (composed on my phone) On May 13, 2010, at 1:22 PM, Viren Patel <vcpatel@emory.edu> wrote:
On 5/13/10 1:14 PM, Rick Westerman wrote:
----- Original Message -----
Hi. I created a workflow to map IGA reads using bowtie and generate a pileup at the end. The workflow is FASTQ Groomer -> Map with Bowtie for Illumina -> SAM-to-BAM -> Generate pileup. I ran the workflow successfully using the built-in mm9 index as reference for both bowtie and the pileup generation. Then I changed the workflow to use a reference file I uploaded (fasta format) and now I get an error on the pileup generation step:
An error occurred running this job: The output file is empty. Your input file may have had no matches, or there may be an error with your input file or settings.
The prior SAM-to-BAM step shows a sizeable BAM file being generated. So I am wondering if the Generate pileup tool requires the reference in a special format.
V. Patel Dept. of Human Genetics Emory University School of Medicine
I am a new Galaxy user but it seems to me that the problem lies with using a built-in index vs. your own fasta file that needs an index built for it. I suspect that the parameters for the workflow are set to use built-in indexes. My suggestion is to manually run the steps instead of relying on the workflow.
I changed the workflow to use my own uploaded reference file, not the built-in index, but judging from the nomenclature I suspect I may have to process (index?) the reference file first into a format usable by the pileup generation tool. However I do not see how I can do that. <vcpatel.vcf> _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user