I am currently trying to find isoMiRS in Illumina RNA-seq libraries and I am currently stuck at the alignment step. I have aligned the trimmed qualified reads to the human pre-miRNAs from miRBase using Bowtie with 3 mismatches. Now I am trying to analyze the BAM files.
How can I make sure that my reads are aligned with a 3 nt extension at the end?
Is there any specific pipeline for this task?
Also, which tools can I use for getting an output similar to the one from the image attached?
Image description :
"Example of small RNA reads aligning to a known miRNA precursor (miR-1-1). The mature miR-1-1 sequence, as annotated in miRBase, is underlined. The minimum free energy secondary structure is denoted by dot-bracket notation, represent complementary bases and represent non-complementary bases. Numbers in the right column represent the abundance of digital read counts corresponding to each sequence."