Filter R1 and its matching R2 based on kmer sequence

Question

[r_mvl]

Hello!

I am working with RNA-seq data, from paired end sequencing (10x precisely, and sequenced on a NextSeq platform).

Basically I have a list of sequences (15 bp long) which are present in only a subset of my R1 reads. What I would like to do is to filter the R2 reads which match this criteria. Do you know how I could achieve this?

Many thanks for your help.

[ATpoint]

Please give a representative example of input and expected output. R1 in 10X are barcodes and UMIs which are not present in R2. It is not clear what you aim to do.

Answer 1

[GenoMax]

You should be able to use bbduk.sh from BBMap suite in filter mode. There is a guide available here.