Hi,
I have used BWA 0.75a to map PE data of WGS to reference, and samtools flagstat to check the resulting BAM file. My pipeline includes the usual sorting, fixing malformed bams, and marking duplicates. I have run this pipeline many times before with no problems, but this one genome had presented something I haven't seen before. The flagstat results are as follows:
36332416 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
32959970 + 0 mapped (90.72%:nan%)
36332416 + 0 paired in sequencing
18166208 + 0 read1
18166208 + 0 read2
354 + 0 properly paired (0.00%:nan%)
32959970 + 0 with itself and mate mapped
0 + 0 singletons (0.00%:nan%)
417710 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
I'm quite confused, as I have nearly 91% of my reads mapping to my reference, but barely any properly pairing. QC analysis (using FastQC) did not show anything out of the ordinary, and the library prep gives an average fragment that we are used to seeing. Is this just literally a case of the reads having no overlap, and we should re-run this particular genome, or can anyone suggest anything else for me to try to get to the bottom of this?
Thanks
I have used BWA 0.75a to map PE data of WGS to reference, and samtools flagstat to check the resulting BAM file. My pipeline includes the usual sorting, fixing malformed bams, and marking duplicates. I have run this pipeline many times before with no problems, but this one genome had presented something I haven't seen before. The flagstat results are as follows:
36332416 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
32959970 + 0 mapped (90.72%:nan%)
36332416 + 0 paired in sequencing
18166208 + 0 read1
18166208 + 0 read2
354 + 0 properly paired (0.00%:nan%)
32959970 + 0 with itself and mate mapped
0 + 0 singletons (0.00%:nan%)
417710 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
I'm quite confused, as I have nearly 91% of my reads mapping to my reference, but barely any properly pairing. QC analysis (using FastQC) did not show anything out of the ordinary, and the library prep gives an average fragment that we are used to seeing. Is this just literally a case of the reads having no overlap, and we should re-run this particular genome, or can anyone suggest anything else for me to try to get to the bottom of this?
Thanks
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