I am trying to create a table for the distribution of mapped RNA sequenced reads across miRBase v.21 for each isomiRs.
I am using contents from this miRBase.mrd file to generate the reads mapped to isomiRs. I have copied the sample output from miRBase.mrd file generated using miRDeep2.
I have written a perl code to identify the isomirs using miRBase.mrd file.
As per the above output, some of the sequenced reads are present in both "ssc-let-7a-1" and "ssc-let-7c".
Note: seq_3228221 is ID and x43 refers to 43 times this sequence present in the FASTQ file.
I am aware that miRDeep2's mapper file uses following bowtie command "bowtie -p 1 -f -n 0 -e 80 -l 18 -a -m 5 --best --strata " to generate the alignment file. This command allows the same sequence to map to multiple miRNAs.
While generating the percentage of mapped reads for all miRNAs, do I need to consider only unique reads (seq_2697760_x253 only once) or reads with multiple matches then it becomes 2*253=506 reads?
For reference, this is the miRDeep2's final read count output file for all miRNAs