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Question: Sample Order in MPileup
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gravatar for hilary.a.edgington
11 weeks ago by
hilary.a.edgington • 0
hilary.a.edgington • 0 wrote:

Hi Galaxy users! I'm attempting to call variants from targeted amplicon sequencing, and ran MPileup on my collection of Bowtie2 aligned reads. The sample names (which were the file names) were replaced in the Mpileup output by "local_bam_0.bam, local_bam_1.bam, local_bam_2.bam...", and I'd like to relabel with my original sample IDs. What is the order in which files are fed into Mpileup when bams are submitted as a collection? Would it be the order they appear in the collection? Alphabetical perhaps?

As a bonus question, what would I have needed to do in order to preserve the sample IDs in the first place?

Any info would be appreciated, thanks!
sample variant mpileup dataset collection • 107 views
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modified 11 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 11 weeks ago by hilary.a.edgington • 0
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gravatar for Jennifer Hillman Jackson
11 weeks ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Add in read group information to the BAMs to have the output labeled informatively. The current mapping tools allow sample (SM) headers to be added to the BAM output at runtime.

To assign sample names when working with collections in Galaxy, please see: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 11 weeks ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen! I appreciate the quick response.

ADD REPLY • link written 11 weeks ago by hilary.a.edgington • 0
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