sample split in multiple flowcells and lanes

Question

[pingu77]

Hi All!

I am analyzing scRNAseq data. Unfortunately, I have the same sample split in multiple flowcells (2) and multiple lanes (2). I have read that there is no problem merging the fastqs files from different lanes. I am wondering if I can then merge the merged fastq (by lanes) by flowcells.

Thank you!

Answer 1

[swbarnes2]

If it's the exact same library, cat it together, no matter how many lanes or flowcells it is distributed on.