Question: What is my RGID, RGLB and RGPU in this read, please?
1
gravatar for Tania
4 months ago by
Tania110
Tania110 wrote:

Hi All

I am confused in extracting the RGID, RGLB and RGPU from this read, any help, thanks?

@E00461:116:AU170602261:1:1101:20456:1415 1:N:0:NTCCAGGT

And if I have each sample is a tumor from a different patient, should I use RGSM as the different sample patient ID?

Thanks

rna-seq • 353 views
ADD COMMENTlink modified 4 months ago by Sharon250 • written 4 months ago by Tania110

That information is not directly in the fastq read header (which is what you have). That information can be derived from this header. See this.

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax46k

I read this tutorial and still confusing. I need to pass this information in step 2.Add read .. in the following tutorial to get my bam, so where can I get the information: https://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq

ADD REPLYlink modified 4 months ago • written 4 months ago by Tania110
1
gravatar for Sharon
4 months ago by
Sharon250
Sharon250 wrote:

Hi Tania

I used this tutorial to get those values from the fastq files, https://angus.readthedocs.io/en/2017/GATK_pipeline.html

Jump to: 4. Add Read group information and do mapping

ADD COMMENTlink written 4 months ago by Sharon250

Amazing, thanks Sharon a lot :)

ADD REPLYlink written 4 months ago by Tania110
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