Question: What is my RGID, RGLB and RGPU in this read, please?
1
gravatar for Tania
2.6 years ago by
Tania130
Tania130 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 • 2.5k views
ADD COMMENTlink modified 2.6 years ago by Sharon480 • written 2.6 years ago by Tania130

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 2.6 years ago • written 2.6 years ago by genomax85k

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 2.6 years ago • written 2.6 years ago by Tania130
2
gravatar for Sharon
2.6 years ago by
Sharon480
Sharon480 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 2.6 years ago by Sharon480

Amazing, thanks Sharon a lot :)

ADD REPLYlink written 2.6 years ago by Tania130
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