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Question: Extracting multiple files with NCBI SRA Tools - BAM Fastq Pileup
2
gravatar for joseph.andrews
18 months ago by
joseph.andrews • 20
Canada
joseph.andrews • 20 wrote:

Hello

I'm trying to import multiple BAM files from NCBI-SRA. A particular sample has 19 runs, each with its own SRR number.

Do I have to import these one at a time, or can multiple SRR accessions be imported simultaneously?

Thanks!
fastq sra ncbi-sra nbci bam • 841 views
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modified 18 months ago by Jennifer Hillman Jackson ♦ 25k • written 18 months ago by joseph.andrews • 20
1
gravatar for Jennifer Hillman Jackson
18 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The NCBI SRA Tools tools retrieve one dataset per retrieval job.

Entering multiple accessions to launch multiple data retrieval jobs could be a future enhancement. I'll make an enhancement request ticket and link it back here as a comment.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k
1

Update: The tool was just updated for multiple accession input. For the input, choose the option to input a list of accessions. Create the list, one accession per line, and upload it to Galaxy then select that dataset.

ADD REPLY • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k
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