I tried to assemble the unmapped reads (mate1/R1 and mate2/R2 using --outReadsUnmapped Fastx ) from STAR alignment using Trinity for Paired-end reads.
By putting the --left unmapped_R1.fastq and --right unmapped_R2.fastq I am getting the error primarily as Error, found read_type 1 but expecting read_type 2 . From the error, it looks (from a discussuion thread) like R1 and R2 are switched for left and right in Trinity. But I am certain, that I used mate1 and R1 and mate2 as R2.
Again if i switched like --left unmapped_R2.fastq and --right unmapped_R1.fastq in Trinity assembly commmand, then it works perfectly. What is the reason behind it? Thank you