I have paired end libraries (prepared by sureselect target enrichments hs protocol) with insert sizes of approximately 150 - 200 bp. A 600 cycle v3 kit was used for sequencing on a MiSeq with the intention of setting the cycle number to 101 x 101 however it was mistakenly set to 301 x 301. When I attempt to correct the read length by adapter trimming to remove the read through there is still a sharp peak of reads close to 300 bp in size. FastQC adapter module tells me there is no adapter left. Is it poor practice to force trim reads down to a certain length?
Try trimming with
bbduk.sh (from the package BBTools / BBMap), using the flags
tbo tpe, which respectively mean trim by overlap (Trim adapters based on where paired reads overlap) and trim pairs evenly (when kmer right-trimming, trim both reads to the minimum length of either). In particular,
tbo is useful for removing adapter even if the sequences are not recognized by the program.
If your reads continue to have a sharp peak of 300bp length, I would not trim them. Are you working with an organism which have an assembled genome? If a reference genome is available, you can check the quality of the reads in relation to base position within reads, using bbmap.sh with the mhist parameter:
mhist=<file> Histogram of match, sub, del, and ins rates by read location.