Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Generate pileup from sra tool produces empty files
0
gravatar for joe.baxter
2.6 years ago by
joe.baxter • 0
ICR, London
joe.baxter • 0 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 COMMENT • link •
modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by joe.baxter • 0
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 2.6 years ago by joe.baxter • 0
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour