Hi is 26% duplicates an extraordinarily high number for single end sureselect targetted SOLiD reads?
Also I presume the duplicates are in part of the mapped reads as well?
I used Picard's markduplicates to arrive at the rmdup bam.
## METRICS CLASS net.sf.picard.sam.DuplicationMetrics
LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
Unknown Library 61303170 0 40652492 26844757 0 0 0.437902
101955662 in total
0 QC failure
26844757 duplicates
61303170 mapped (60.13%)
0 paired in sequencing
0 read1
0 read2
0 properly paired (nan%)
0 with itself and mate mapped
0 singletons (nan%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
Also I presume the duplicates are in part of the mapped reads as well?
I used Picard's markduplicates to arrive at the rmdup bam.
## METRICS CLASS net.sf.picard.sam.DuplicationMetrics
LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
Unknown Library 61303170 0 40652492 26844757 0 0 0.437902
101955662 in total
0 QC failure
26844757 duplicates
61303170 mapped (60.13%)
0 paired in sequencing
0 read1
0 read2
0 properly paired (nan%)
0 with itself and mate mapped
0 singletons (nan%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
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