I have a paired-end dataset and want to pool it to map all reads altogether. I couldn't find the tool which can be used for it.
Thanks a lot in advance!
If you are talking about interleaving paired-end reads from individual files into a single file, BBMap is your friend:
reformat.sh in=reads_1.fastq in2=reads_2.fastq -out=paired_reads.fastq
Thank you! I will try to.
Be sure that the aligner has an option to support paired-end interleaved reads.
Can you explain pooling? Paired-end reads consist of R1 and R2 and these must be mapped with a dedicated paired-end aligner. You cannot simply combine R1 and R2 and treat them as single-end reads.