Hello all,
I merged two ELAND export files by using samtools, but samtools flagstat shows that
191134982 in total
0 QC failure
0 duplicates
139825529 mapped (73.16%)
191134982 paired in sequencing
95567491 read1
95567491 read2
0 properly paired (0.00%)
115989136 with itself and mate mapped
23836393 singletons (12.47%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
Why it shows 0 properly paired?
Couldn't run picard MarkDuplicates, thread exception:
Exception in thread "main" java.lang.NullPointerException
at net.sf.picard.sam.DiskReadEndsMap.remove(DiskReadEndsMap.java:87)
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:289)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:126)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:143)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:105)
Any help? Many thanks.
I merged two ELAND export files by using samtools, but samtools flagstat shows that
191134982 in total
0 QC failure
0 duplicates
139825529 mapped (73.16%)
191134982 paired in sequencing
95567491 read1
95567491 read2
0 properly paired (0.00%)
115989136 with itself and mate mapped
23836393 singletons (12.47%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
Why it shows 0 properly paired?
Couldn't run picard MarkDuplicates, thread exception:
Exception in thread "main" java.lang.NullPointerException
at net.sf.picard.sam.DiskReadEndsMap.remove(DiskReadEndsMap.java:87)
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:289)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:126)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:143)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:105)
Any help? Many thanks.
Comment