Flagstat results: 0 reads

Question

[rmande]

Hi,

I ran samtools flagstat on a bam file I aligned from paired end fastqs using bwa-mem and this is the result I got.

141275694 + 0 in total (QC-passed reads + QC-failed reads)
6641948 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
1136170314 + 0 mapped (99.55% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

I don't understand why > 99% of reads would be mapped correctly but 0 would be paired in sequencing, properly paired, etc. Could someone point me as to what went wrong with the alignment?

Thank you.

[Devon Ryan]

Presumably you didn't align them as paired-end, but rather multiple single-end files. samtools flagstat is just reporting what the aligner output, so the problem is either with the aligner or how you used it.

[dariober]

Have a look at, and maybe post, the header of the bam file which you can extract with samtools view -H myAln.bam. The line(s) starting with @PG should contain the command that was used to align the reads. This will tell you whether bwa was run in single or paired-end mode.

[pld]

I just had this problem, did you supply the forward or reverse file twice?