I have a BED file (GSM1097888) like following:
chr1 17146 17163 t0062322_2 255 -
And now I am trying to calculate the RPM for miRNA based on this (Illumina HiSeq 2000 for smallRNA) data. I used miRNA annotation (hsa.gff3) from miRBase, with conversing to bed file firstly. Then I applied bedmap tool (bedmap --echo --echo-map --count hsa.bed seq.bed > result.bed) to map and count the reads for each miRNA. Finally I only get expression for 133 miRNAs, compared to more than 4000 in hsa.bed. As well, the total mapped read number is much less than the original one (14,000 vs 200,000). Would you please tell me if my analysis is correct?