Merging BAM files after alignment or restarting the workflow?

Question

[stanmih2]

Hello,

I have about 50 samples to analyze in an RNA-seq workflow. I've just realized that some of the samples were sequenced on multiple lanes (L001, L002), but they share the same sample name. I’ve already reached the featureCounts step, but I didn’t merge the FASTQ files for these samples at the beginning.

My question is: can I merge the BAM files for the corresponding lanes after alignment and continue the analysis from this point? Or would it be better to restart everything from the beginning, starting with a FASTQ merge?

Thank you for your help!

Answer 1

[GenoMax]

Yes you can merge the lane specific aligned BAM files. You will need to re-do the counting with featureCounts for the merged files.