Samtools Flagstat Comments

0

Hi, I am trying to solve total alignments :0 results of featureCounts this problem. Now I checked my bam files with that command samtools flagstat .bam. What do you think about these results? Is this possible?

11214947 + 0 in total (QC-passed reads + QC-failed reads)
5640993 + 0 secondary
108597 + 0 supplementary
0 + 0 duplicates
11214947 + 0 mapped (100.00% : 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)


Samtools


BAM


Rna-Seq


Alignment

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