Question: What is my RGID, RGLB and RGPU in this read, please?
1
gravatar for Tania
13 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 • 928 views
ADD COMMENTlink modified 13 months ago by Sharon390 • written 13 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 13 months ago • written 13 months ago by genomax60k

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 13 months ago • written 13 months ago by Tania120
1
gravatar for Sharon
13 months ago by
Sharon390
Sharon390 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 13 months ago by Sharon390

Amazing, thanks Sharon a lot :)

ADD REPLYlink written 13 months ago by Tania120
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