Running samtools flagstat on a bam file resulting from alignment with Hisat2 gives:
Shouldn't there be 100% mapping? I think because of this I also get the warning described below.
I also notice this warning at the end of an HTSeq-count log file when counting features in the same alignment file above:
Should I be worried about this warning? Note that the same raw reads aligned with Tophat2 had 100% mapping in the respective bam file.
Code:
76075665 + 0 in total (QC-passed reads + QC-failed reads) 1565341 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 71435955 + 0 mapped (93.90% : N/A) 74510324 + 0 paired in sequencing 37255162 + 0 read1 37255162 + 0 read2 64430312 + 0 properly paired (86.47% : N/A) 67187398 + 0 with itself and mate mapped 2683216 + 0 singletons (3.60% : N/A) 2452092 + 0 with mate mapped to a different chr 2095660 + 0 with mate mapped to a different chr (mapQ>=5)
I also notice this warning at the end of an HTSeq-count log file when counting features in the same alignment file above:
Code:
Warning: 284233 reads with missing mate encountered.
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