I am in the process of writing a script to automate small RNA-seq data analysis (18-30nt read length) to identify miRNAs and other types of small RNAs. Based on my reading this is what I came up with.
- Trim adaptors with Cutadapt.
- Alignment using Bowtie v1 (old version, not bowtie2).
- Count miRNAs using featureCounts (in the case of miRNA).
Does this look good? If not what other steps are recommended?
Thanks in advance,