Tools for hard trimming?

Question

[v.berriosfarias]

Hello I need help to apply hard trimming to my Paired-end reads, (20nt at 5´and same nts for 3´ across all my reads)

looking in a paper it seems that bbmap could be useful for this but I'm not sure and cannot find a tutorial on hard trimming reads

If someone can list some tools for this purpose and/or well-explained tutorials ill be so thankful :D

Answer 1

[h.mon]

You want bbduk with the "force trim" parameters:

forcetrimleft=0     (ftl) If positive, trim bases to the left of this position
                    (exclusive, 0-based).
forcetrimright=0    (ftr) If positive, trim bases to the right of this position
                    (exclusive, 0-based).
forcetrimright2=0   (ftr2) If positive, trim this many bases on the right end.

Why do you need this hard trimming? If you want to remove primers, this is not the best way to proceed.

[v.berriosfarias]

yesss i used this and worked for me!

Thanks

[v.berriosfarias]

the primers are part of the read? didnt know that, I was concerned about the adapters, but the fastqc report show no info of adapter sequences, nevertheless at the end of the sequences I got an irregular "per base sequence content" line patterns. So hard trimming is what I thought that could help on this,

Answer 2

[igor]

If you want to trim a specific number of bases, you can try FASTX-Toolkit or seqtk which are designed for simple FASTQ manipulations like that.

Answer 3

[5heikki]

I would just use awk for this..

[igor]

It's possible to have multi-line FASTA/FASTQ files. In that case, this becomes substantially more challenging.

[5heikki]

Sure, however, in +10 years I'm yet to see a single fastq file that doesn't follow the 4 lines per sequence format..

[igor]

Consider yourself lucky.