Hello, is there anyone aware of the difference in remove duplicate reads by using different tools. For example, the number of duplicate reads removed by cd-hit-454 and PRINSEQ is much different. Thanks.
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you may try Picard to do this -
I know samtools rmdup and picard markdup.
A: samtools rmdup does not remove interchromosomal duplicates. MarkDuplicates does remove these duplicates.
Samtools paired-end rmdup does not work for unpaired reads (e.g. orphan reads or ends mapped to different chromosomes). If this is a concern, please use Picard’s MarkDuplicate which correctly handles these cases, although a little slower.Comment
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Can somebody show how pickard does duplicate markups and how you can remove them? I can't seem to find the markings....?
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