How to remove some sequences

[k_a_r_o_l]

Hello,

Maybe someone can help me. Do You know any software, method how to remove from FASTQ files reads with certain motif. I dont want to trimm my reads but rather remove whole sequences with specific motifs.

Thx

[GenoMax]

Can you post an example of the header's you want to remove?

[k_a_r_o_l]

My library has a lot of short inserts, and this is why some of my reads have nextera transposase sequence in it. Depending on insert I observe different lengths of nextera sequences in my reads so it is hard to perform a specific trimming. I dont want to trimm all my reads. This is why I think that better will be to remove all reads with the nextera sequence from my data.

[GenoMax]

One option would be to use BBDuk and provide the sequence of nextera transposases as literal="nextera_sequence" option.

Edit: You will need to add outm1 (and optionally outm2, if you have paired-end reads) options to move the entire reads that match the transposase sequence to new files (specified by outm1 and outm2) leaving cleaned reads in out1= (and out2=) files.

[ClemBuntu]

What about cutadapt using "--discard-trimmed" option ? Otherwise it should be possible with grep command and -v option.