I'm doing an RNAseq analysis and encounter an error when trying to perform featureCounts using Subread tool.
The error is the following:
ERROR: No paired-end reads were detected in paired-end read library.
and this is the command and the parameters:
featureCounts -T 8 -p -a Salmonella.gff3 -t CDS,exon,rRNA,tmRNA,tRNA -g ID -o counts.txt 1.bam
however if I omit the parameter -p the data is processed, but I'm not sure if what I receive is correct (e.g. double counting of the reads?).
A bit of background:
- the sequencing data was paired-end
- the mapping of the sequenced reads to respective genome was performed using bowtie2; 1 output BAM file was produced (I suppose paired-end reads were merged into 1 file) from 2 input files containing paired end reads
So my question is whether is it correct to omit the -p parameter and process the data as single end reads? If not, what should I do?