Hi,
I have an IonTorrent output but the provider doesn't want to give information about primer sequences. Instead it gives a bed file includes regions of interest. So if I do alignment and bedtools intersect than trimming sequences by outside parts which is not in the region, I'm not comfortable this is a good approach. We want to use the output as a data for finding SNP frequencies and for the best approach primer sequences must be trimmed.
So, is there a way to do this job properly? I mean is there a way to trim sequences with no knowledge about primers?
I have an IonTorrent output but the provider doesn't want to give information about primer sequences. Instead it gives a bed file includes regions of interest. So if I do alignment and bedtools intersect than trimming sequences by outside parts which is not in the region, I'm not comfortable this is a good approach. We want to use the output as a data for finding SNP frequencies and for the best approach primer sequences must be trimmed.
So, is there a way to do this job properly? I mean is there a way to trim sequences with no knowledge about primers?
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