Hi all, I am new to smRNA processing and wanted to...
# smrnaseq
t
Hi all, I am new to smRNA processing and wanted to make sure I am interpreting the output correctly in the multiQC. Specifically, the
mature_hairpin_genome
are reads aligned to mature miRNA database + hairpin database + reference genome. A high mapping percentage of
mature_hairpin_genome
relative to
mature
and
mature_hairpin
would otherwise indicate that the majority of reads are mapping to regions of the genome outside of known mature miRNAs and precursors
I looked into the pipeline a bit more, and it looks like my presumption above is incorrect. Tracing back the bowtie reference built with the hairpin.fa (i.e only hairpins). Is there a reason why the output gets labeled
mature_hairpin
? Or am I mistake again ?
bowtie-build --threads 12 hairpin.fa_igenome.fa_idx.fa bowtie/hairpin