featureCounts paired end reads wrongly assigned on the single end mode

featureCounts paired end reads wrongly assigned on the single end mode

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Hello!
I have RNAseq data from samples containing 2 to 3 bacterial strains each. For the analysis I performed FastQC, trimmomatic to remove adapters and then Bowtie2 to align the reads to the reference genomes. I have one bowtie2 output file per sample with the paired ends and another one with the singles. I want to make one output file per reference genome with featurecounts for the paired ends on one side and the singles on the other.

For the paired end I run this command :
featureCounts -T 24 -p -M -g Parent -a $x -o ${Output}/${genome}.txt ${Samples}/${genome}_paired

In output I get this:
enter image description here

I don’t understand why in the running featurecounts part assign them in single end mode ?

when I look at one of the paired end input files I get this:

97320876 + 0 in total (QC-passed reads + QC-failed reads)
97320876 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
591739 + 0 mapped (0.61% : N/A)
591739 + 0 primary mapped (0.61% : N/A)
97320876 + 0 paired in sequencing
48660438 + 0 read1
48660438 + 0 read2
499606 + 0 properly paired (0.51% : N/A)
518434 + 0 with itself and mate mapped
73305 + 0 singletons (0.08% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)


featureCounts

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