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.
-
-
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
-
Can somebody show how pickard does duplicate markups and how you can remove them? I can't seem to find the markings....?
NashComment
-
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment