Question: Generate pileup from sra tool produces empty files
gravatar for joe.baxter
2.6 years ago by
ICR, London
joe.baxter0 wrote:

I'm currently trying to generate pileup files for a gene from sra archives of many RNA-seq experiments. At the moment, regardless of the parameters entered, I am always returned an entirely empty file - no error, it just says that the job is finished.

I've managed to generate FASTQ files from these same archives so I know there's data there. I've tried all possible ways of selecting my gene of interest, including leaving the aligned region blank. All give me the same, blank output.

I'd be grateful for any suggestions of how to extract a pileup file from sra, either using this tool or alternatives!

fastq sra pileup • 771 views
ADD COMMENTlink modified 2.6 years ago by Jennifer Hillman Jackson25k • written 2.6 years ago by joe.baxter0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Download the BAM then run Mpileup/pileup directly on that dataset.

Many times the BAM datasets from SRA are tool large to run through this particular tool plus there is limited control over parameters.

I ran some tests on this tool a few weeks ago, but will revisit them to make sure there is not a current problem with the tool itself. If something is uncovered, I will share a link to the issue ticket as a followup reply.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k

Thanks Jen. Do you know what the size limit for the BAM files would be?

ADD REPLYlink written 2.6 years ago by joe.baxter0
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