

##### RSEM ###############

mkdir rsem
mkdir index_rsem

rsem-prepare-reference --bowtie --gtf Homo_sapiens.GRCh38.88.gtf Homo_sapiens.GRCh38.dna.chromosome.22.fa index_rsem/human_22_rsem

rsem-calculate-expression -p 1 --no-bam-output --paired-end reads.1.fastq reads.2.fastq --forward-prob 0 index_rsem/human_22_rsem rsem/expression


##### SALMON ###########

mkdir salmon
mkdir index_salmon

wget ftp://ftp.ensembl.org/pub/release-88/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
gunzip Homo_sapiens.GRCh38.cdna.all.fa.gz
mv Homo_sapiens.GRCh38.cdna.all.fa human_transcriptome.fa 

salmon index -p 4 -t human_transcriptome.fa –i index_salmon/human_transcriptome_salmon

salmon quant -p 4 --useVBOpt -i index_salmon/human_transcriptome_salmon -l ISR -1 reads.1.fastq -2 reads.2.fastq --geneMap Homo_sapiens.GRCh38.88.gtf -o salmon/expression
