How to choose the right RG,SM and LB values for alignment

Question

[Ric]

I have the following FASTQ files:

• 0000-C1_S7_L001_R1.paired.fastq.gz
• ...
• 0000-C1_S7_L004_R1.paired.fastq.gz

I am not quite sure which RG, SM and LB correct:

@RG     ID:0000-C1_S7_L001      SM:0000-C1_S7      LB:batch1      PL:ILLUMINA
...
@RG     ID:0000-C1_S7_L004      SM:0000-C1_S7      LB:batch1      PL:ILLUMINA

or

@RG     ID:0000-C1_S7_L001      SM:0000-C1_S7_L001      LB:0000-C1_S7_L001      PL:ILLUMINA
...
@RG     ID:0000-C1_S7_L004      SM:0000-C1_S7_L004      LB:0000-C1_S7_L004      PL:ILLUMINA

Which one to choose from or bothe above solutions are wrong?

Thank you in advice

Answer 1

[Devon Ryan]

Whether LB should be the same depends on whether the libraries were the same on each lane (they probably were, so LB:batch1 or LB:0000-C1_S7 would work). Regardless, these are presumably the same sample, so 'SM:0000-C1_S7` for both.