I apologize for such a question, but should we use all the generated FASTQ files (including failed ones to merge) for the alignment? Or do you suggest using only the successfully merged fastq files?
We generally map the merged as single-end and the unmerged as paired-end, sort each and merge. You can do this in one line using file descriptors actually.
I apologize for such a question, but should we use all the generated FASTQ files (including failed ones to merge) for the alignment? Or do you suggest using only the successfully merged fastq files?