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Old 09-04-2012, 09:32 AM   #1
Location: beijing

Join Date: Nov 2011
Posts: 17
Default about picard markduplicate

hi all, sorry, but I'm afraid I have to ask you a naive and stupid question about removing dupilicates after marking duplicates with picard.

After marking duplicates with picard, I then used "samtools view -F 1024 -bh bamfile >> filtered bamfile" to remove duplicates.

But a question came to my mind: are all the reads with same start and end will be removed using my protocal? It seems at least one of them should be left in my bamfile.

Thanks a lot!
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