RNAsik-pipe
This is fully SIcK way towards differential gene expression !
RNAsik-pipe implemented in BigDataScript (bds) language.
IF( SuperQuickStart ) {
RNAsik -fqDir https://bioinformatics.erc.monash.edu/home/kirill/sikTestData/rawData/fqFiles.txt \
-align star \
-fastaRef ftp://ftp.ensembl.org/pub/release-91/fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa.gz \
-gtfFile ftp://ftp.ensembl.org/pub/release-91/gtf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.91.gtf.gz \
-counts \
-paired \
-all
}