RNA-Seq of Yarrowia lipolytica : overproducing extracellular YFP
Removal of adapters using Cutadapt. Standard filtering using quality paramter q25 and minimal reads length m15. Quality reports generated using FASTQC. Mapping to a reference genome (NCBI GCF_000002525.2) done with Hisat2 (only reads > m20). Hisat was run with a library generation option (-rna-strandness RF) and splicing variants identification (-novel-spicesite-outfile-). HTseq was used for counting of total read pairs mapped to individual genes (differentaiting + and - strands). Gene annotationas were assigned based on gtf file for the reference genome.