Entering edit mode
5.7 years ago
a.rex
▴
350
I have run this command on my bam file (it has already gone through MARKDUP):
java -jar picard.jar EstimateLibraryComplexity INPUT=lib.bam OUTPUT=sample_libcomp.txt
I get this output:
## METRICS CLASS picard.sam.DuplicationMetrics
LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
Unknown 0 15424936 0 0 0 13638 2 0.000884 8719138504
## HISTOGRAM java.lang.Integer
duplication_group_count Unknown
1 15398401
2 12287
3 514
4 71
5 17
6 6
7 2
8 1
9 1
Does this mean that I have 15398401 reads with no other duplicates (i.e. 15398401 that appear once)? I have looked on other blogs and the histogram first column represents duplicate sets?