What is my RGID, RGLB and RGPU in this read, please?
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
1 answer
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
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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.
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