fastq-mcf for removing target specific primer sequences

[daie...@yahoo.com]

Hello,

Is fastq-mcf an appropriate tools for clipping target specific primer sequences in an amplicon sequencing experiment? This particular experiment contains overlapping amplicons.  If so, what setting should be used?  Thanks.

[Erik Aronesty]

I would not use fastq-mcf to trim primer sequences.   Primers will be present in their entirety, whereas adaptors are only partially present, if at all.   The best example of highly necessary and high-quality adatptor trimming is when you're doing miRNA (21bp sequences with 35bp or 50bp reads), where partial adaptors are present on every read.   

I would just align with something like bwamem against the primers, remove the aligned bits, and then re-align against the genome.   (don't align to targetome! )