I've performed an alignment using Bowtie on small RNAseq reads (22-50 nt) from total RNA-Seq sequencing experiment. I got almost 90% of multiple mapped reads. Then, I counted the reads per biotype (gtf file from Ensembl) using mmquant program (which is designed for counting tasks in the case of high rate of multiple mapping reads, HTSeqcount and featureCounts don't take into account the multiple mapped reads, that is why I've used mmquant). After getting the matrix of count, and using a shell script I was able to count the reads per biotype class (protein_coding, lincRNA, rRNA, ...). I got like 80% of the alignments falling in intergenic regions (lincRNA), and only 6% of my reads correspond to protein_coding !!!
Can I continue downstream analysis with such results ?
Any idea ?