Features:
QC: cutadapt adapter trimming; fastqc pre- and post-adapter trimming; kraken; fastqscreen (standard seqs and short RNAs); multiqc
Alignment with mirdeep2: mapping/collapsing; 2 pass alignment (annotated and de novo)
Quantification and DEG: edgeR
Features: QC: cutadapt adapter trimming; fastqc pre- and post-adapter trimming; kraken; fastqscreen (standard seqs and short RNAs); multiqc Alignment with mirdeep2: mapping/collapsing; 2 pass alignment (annotated and de novo) Quantification and DEG: edgeR