Hi all -
I'm wondering what methods you'd recommend to remove primer sequences from amplicon sequencing data where multiple amplicons for the same specimen in the same run will overlap. Simply removing the primers using one of the trimming tools seems like it will appropriately remove the primers for the amplicon they are producing, but also any neighboring sequence in an adjacent amplicon which overlaps the sequence.
One strategy I had thought might work is to align the reads to each amplcon sequence separately, and process them like that, but I was hoping there might be an easier way. I'm also concerned that since the amplicons overlap that reads will inappropriately align to the incorrect amplicon, depending on the order they're processed.
Please forgive me if there is an obvious and well known solution to this, I did search for quite a while.
Thanks in advance!
I'm wondering what methods you'd recommend to remove primer sequences from amplicon sequencing data where multiple amplicons for the same specimen in the same run will overlap. Simply removing the primers using one of the trimming tools seems like it will appropriately remove the primers for the amplicon they are producing, but also any neighboring sequence in an adjacent amplicon which overlaps the sequence.
One strategy I had thought might work is to align the reads to each amplcon sequence separately, and process them like that, but I was hoping there might be an easier way. I'm also concerned that since the amplicons overlap that reads will inappropriately align to the incorrect amplicon, depending on the order they're processed.
Please forgive me if there is an obvious and well known solution to this, I did search for quite a while.
Thanks in advance!
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