Question: Is it possible to pool the paired-end data?
0
gravatar for tanya_fiskur
5 weeks ago by
tanya_fiskur30
tanya_fiskur30 wrote:

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 • 120 views
ADD COMMENTlink written 5 weeks ago by tanya_fiskur30
1

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 REPLYlink written 5 weeks ago by Mensur Dlakic5.8k

Thank you! I will try to.

ADD REPLYlink written 5 weeks ago by tanya_fiskur30

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

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by ATpoint36k

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 REPLYlink modified 5 weeks ago • written 5 weeks ago by ATpoint36k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1636 users visited in the last hour