Is it possible to pool the paired-end data?

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4.7 years ago

tanya_fiskur ▴ 70

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!

RNA-Seq • 1.1k views

ADD COMMENT • link 4.7 years ago by tanya_fiskur ▴ 70

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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

ADD REPLY • link 4.7 years ago by Mensur Dlakic ★ 28k

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Thank you! I will try to.

ADD REPLY • link 4.7 years ago by tanya_fiskur ▴ 70

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

ADD REPLY • link 4.7 years ago by ATpoint 86k

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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.

ADD REPLY • link 4.7 years ago by ATpoint 86k

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