Question: How Should I Trim My FASTQ File Now That I Merged Paired-End Reads
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gravatar for isu2017
12 weeks ago by
isu20170
isu20170 wrote:

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!!

paired-end fastq • 192 views
ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by isu20170

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.

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by genomax76k

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.

ADD REPLYlink written 12 weeks ago by isu20170

Do you know why they want to have trimmed reads?

ADD REPLYlink written 12 weeks ago by finswimmer13k

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

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by genomax76k
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