I used tophat to map my RNAseq reads to human genome hg19 (My data is single-end) and I got some files in the tophat output folder. I need to know how many reads mapped to the reference genome and how many don't mapped and the percentage of overall alignment.
BTW, I used the following samtools command
samtools flagstat accepted_hits.bam
and It gave me the following results:
175638490 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 175638490 + 0 mapped (100.00%:-nan%) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (-nan%:-nan%) 0 + 0 with itself and mate mapped 0 + 0 singletons (-nan%:-nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)
Any explanation of the zeros above