Hi,
On running the samtools flagstat command on the accepted_hits.bam file generated by tophat, I get the following output:
13414556 in total
0 QC failure
0 duplicates
13414556 mapped (100.00%)
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)
I am not sure why the duplicates are 0, as this run of tophat allws upto 40 mismatches and there are reads which are mapped to several location on the genome.
Could someone tell me if there is an alternate way to find out the number of unique reads and the distribution of multi mapped reads from the bam file?
Thanks you.
On running the samtools flagstat command on the accepted_hits.bam file generated by tophat, I get the following output:
13414556 in total
0 QC failure
0 duplicates
13414556 mapped (100.00%)
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)
I am not sure why the duplicates are 0, as this run of tophat allws upto 40 mismatches and there are reads which are mapped to several location on the genome.
Could someone tell me if there is an alternate way to find out the number of unique reads and the distribution of multi mapped reads from the bam file?
Thanks you.
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