Trim 3' ends from single-end reads

Question

[Maria]

Hi,

I have fastq sequences with reads that contains 6 pairs of different primers. They are single-end reads of 200-220 bp (aprox.), and I found forward and reverse primers in my reads. I would like to trim both ends, just removing 21 bp at 5' end and 24 bp at 3' end. Any help would be really appreciated.

[Maria]

Thank you both for your help! The two approaches have worked well!

[GenoMax]

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

Answer 1

[GenoMax]

You can use bbduk.sh from BBMap suite to do this. Options you will need is

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.

A guide is available for BBDuk.

Answer 2

[rodolfo.peacewalker]

Hi Maria!

Did you try to use Trimmomatic? CROP and HEADCROP options allow you to trim your reads at 3' and 5' ends, respectively. With CROP <length> option you specify the max length of your reads before trimming at 3' end. In your case 196 for the 220 bp reads or 176 for 200 bp reads. Then, use HEADCROP <length> specify the number of bases to trim at 5' end, in this case 21.

Run something like this:

path_to_trimmomatic/trimmomatic SE path_to_input_files/input.fq path_to_output_files/output.fq CROP:196 HEADCROP:21

This link is for trimmomatic user's guide.