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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. -- Rick Westerman westerman@purdue.edu Bioinformatics specialist at the Genomics Facility. Phone: (765) 494-0505 FAX: (765) 496-7255 Department of Horticulture and Landscape Architecture 625 Agriculture Mall Drive West Lafayette, IN 47907-2010 Physically located in room S049, WSLR building