HI:
I use CREST to find SV in cancer genome by whole genome sequencing (illumina paired-end 90bp, the length of fragment is ~600bp).
In CREST.pl a parameter called rmdup which is removing duplicate reads or not and default was remove. but the final results (html file) show many same reads and aligned to the same position. and I check those reads pairs manually and found all those reads pairs aligned to the same position which I think may come from PCR and called dupicates, why they don`t be removed even program tell me they could be removed.
I use CREST to find SV in cancer genome by whole genome sequencing (illumina paired-end 90bp, the length of fragment is ~600bp).
In CREST.pl a parameter called rmdup which is removing duplicate reads or not and default was remove. but the final results (html file) show many same reads and aligned to the same position. and I check those reads pairs manually and found all those reads pairs aligned to the same position which I think may come from PCR and called dupicates, why they don`t be removed even program tell me they could be removed.