Is it possible to pool the paired-end data?

Question

[tanya_fiskur]

Hello everyone.

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. Any suggestions?

Thanks a lot in advance!

[Mensur Dlakic]

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

[tanya_fiskur]

Thank you! I will try to.

[ATpoint]

Be sure that the aligner has an option to support paired-end interleaved reads.

[ATpoint]

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.