Question: What is my RGID, RGLB and RGPU in this read, please?
1
gravatar for Tania
10 months ago by
Tania120
Tania120 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 • 734 views
ADD COMMENTlink modified 10 months ago by Sharon340 • written 10 months ago by Tania120

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 10 months ago • written 10 months ago by genomax57k

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 10 months ago • written 10 months ago by Tania120
1
gravatar for Sharon
10 months ago by
Sharon340
Sharon340 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 10 months ago by Sharon340

Amazing, thanks Sharon a lot :)

ADD REPLYlink written 10 months ago by Tania120
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