Entering edit mode
22 months ago
priya.bmg ▴ 60
I am trying to run the following command to align the read with reference using bwa-mem, but, keep getting the error:
[E::bwa_set_rg] no ID at the read group line
This is the header of my fastq file:
This is command used to run the alignment
bwa-mem2 mem -t 8 -R @RG\tID:A00684\tLB:110\tPL:ILLUMINA\tSM:H2TYCDMXY\ /scicore/home/cichon/GROUP/bwa-mem2/gch38.fa DE98NGSUKBD117612_1_1.fq DE98NGSUKBD117612_1_2.fq > aligned.sam
I am bit lost. What is the tID, t LB, tPM and t SM in the fastq file. How to get the read group info frm fastq file
Read group information can be found via GATK help pages. Read groups are not absolute. You may need to make up some of the strings yourself. What is critical is that replicates should be clearly identifiable (e.g.
Thank you. I referred the GATK page. Could you provide an example of how to get the SM group info?. How to get the DNA library preparation identifier info, LB?
You know which samples you are working with so use the right names. This is clearly described in link above for
LBif same library was run on multiple lanes then the
nameyou use just need to be identical.