Paired-end reads somehow counted twice?

Paired-end reads somehow counted twice?


Hi. I’m new in Bioinformatics and try to extract read counts from fastq files.

I compared my result with answer count matrix, and read counts are doubled.

enter image description here

(Left one is from the answer read count matrix, and right one is my result.)

I used these commands on ubuntu to get my result:

Could you please tell me what went wrong?

hisat2 -p 50 
-x [ENSEMBL refrence file] 
-1 [fastq file_1] 
-2 [fastq file_2] 
-S [output file name].sam

samtools sort -@ 8 -o [output file name].bam [input file name].sam

featureCounts -p -T 10 -a [GTF file] 
-o [output file name] 
[input file name].bam

I think I didn’t apply pair-end option in some commands but I couldn’t figure out which one.





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