Remove pattern from NGS reads in a fastq file

Question

[ATGTAA]

Hi Community,

A complete newbie to this all and I am not able to find a solution to my problem.

I have PE NGS as R1 and R2 reads that I merged with BBmerge.sh and extracted all reads that match a pattern using seqkit grep --by-seq --ignore-case --use-regexp --pattern XXXX

The pattern is in the centre of the read [variable 35bps]-[constant XXX]-[variable 40bps].

Now I want to remove the constant region and fuse the two variables:

before: [variable 35bps]-[constant XXX]-[variable 40bps]

after: [variable 35bps]-[variable 40bps]

I have tried trimming tools but as far as I can tell remove everything up and including the adaptor which in my case is the constant region.

Any tool out there that can be suggested ?

Thank you for the help!

Answer 1

[colindaven]

Have a look at sed and awk

https://stackoverflow.com/questions/24469977/replace-particular-string-at-fixed-position-using-sed

https://linuxize.com/post/how-to-use-sed-to-find-and-replace-string-in-files/

Or if you prefer a more bioinformatics solution, seqkit subseq looks good for your needs

https://bioinf.shenwei.me/seqkit/usage/#subseq

[shenwei356]

You mean seqkit replace? which could be used to remove the constant subsequence:

seqkit replace -i -s -p xxxxxxx test.fq.gz -o clean.fq.gz