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Fastqs different lanes

Can anyone please confirm the following.

  • You should generate sam/bams with read groups for downstream analysis (GATK)

  • If you have fastqs from the same sample run over different lanes of the flowcell these would have different read groups

  • Therefore you should keep the fastqs seperate, align whilst adding read groups and then merge after alignment.

  • By concatenating fastqs before the alignment step you would lose the read group information.

fastq
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updated by benformatics benformatics • written by samuel samuel

2 answers

Fastqs don't have read groups. The same sample split across different lanes can all be catted together as fastqs.

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written by swbarnes2 swbarnes2

I'm aware fastqs don't have read groups and that we can add them at the alignment stage. I was wondering as to whether we need to preserve lane information for downstream applications such as MarkDuplicates i.e. when marking optical duplicates?

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written by samuel samuel

Follow the GATK standards probably:

https://gatk.broadinstitute.org/hc/en-us/articles/360035889471-How-should-I-pre-process-data-from-multiplexed-sequencing-and-multi-library-designs-

Note that for the purposes of marking duplicates you would merge the lanes as the libraries themselves contain PCR duplicates across lanes.

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written by benformatics benformatics

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