Question: Flagstat results: 0 reads
0
gravatar for rmande
3.4 years ago by
rmande0
rmande0 wrote:

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.

next-gen alignment genome • 1.3k views
ADD COMMENTlink modified 3.4 years ago by pld4.8k • written 3.4 years ago by rmande0
1

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.

ADD REPLYlink written 3.4 years ago by Devon Ryan93k
1

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.

ADD REPLYlink written 3.4 years ago by dariober10k

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

ADD REPLYlink written 3.4 years ago by pld4.8k
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