Question: What is my RGID, RGLB and RGPU in this read, please?
0
gravatar for Tania
5 weeks ago by
Tania50
Tania50 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 • 170 views
ADD COMMENTlink modified 5 weeks ago by Sharon130 • written 5 weeks ago by Tania50

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 5 weeks ago • written 5 weeks ago by genomax40k

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 5 weeks ago • written 5 weeks ago by Tania50
1
gravatar for Sharon
5 weeks ago by
Sharon130
Sharon130 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 5 weeks ago by Sharon130

Amazing, thanks Sharon a lot :)

ADD REPLYlink written 5 weeks ago by Tania50
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