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!!