How Should I Trim My FASTQ File Now That I Merged Paired-End Reads

Question

[isu2017]

I have paired-end read files (fq_1 and fq_2.) Our kit mentions to trim them as follows:

Trim 15BP from the right side (or 3" end) of read 1 (fq_1) and trim 15BP from the left side (or 5" end) of read 2 (fq_2.)

seqtk trimfq -e 15 fq_1 > fq_1_trimmed
seqtk trimfq -b 15 fq_2 > fq_2_trimmed

However, because our downstream meta-genomics software does not accept paired-end reads, I have decided to merge the paired-end FASTQ files into one.

./bbmerge.sh in=fq_1 in2=fq_2 out=fq_merged

However, I am confused as to how I now should trim this merged FASTQ, based upon the kit recommendations.

Any help would be great!!

[GenoMax]

I would suggest following instructions from your kit since some downstream analysis may be dependent on how the reads are initially processed. You could try and see if you can merge the reads after they are trimmed.

[isu2017]

I think that's probably what I'm going to end up doing, because the kit recommends trimming before any downstream analysis (and does not mention how to handle a situation like this.) Although I normally wouldn't really consider merging paired-FQ as "downstream", but we are interested in seeing how these merged results compare to results we have gotten using the reads by themselves in our downstream software.

[finswimmer]

Do you know why they want to have trimmed reads?

[GenoMax]

Sometimes kits will add extra bases via the adapters used which would need to be trimmed before analysis.