For RNA-seq analysis RNAcocktail pipelines were used.
Pipelines:
- raw_reads -> SALMON-SMEM -> DESeq2
- raw_reads -> HISAT2 -> Stringtie -> Ballgown
For first pipeline two results are obtained: with and with out quality check control for reads. Pipeline #1 with out quality check was performed on ensembl transcriptome annotation version 67 (version 92 is available).