# Creating index
# https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/
# salmon index -t gentrome.fa.gz -d decoys.txt -p 16 -i salmon_index --gencode


for f in /home/reimonnt/DE-to-HB/JHG_RNA-seq/*R1_001.fastq.gz
do
salmon quant -i /home/reimonnt/rnaseq-4dn-hepdff/salmon_index \
	-l A -1 $f -2 ${f%1_001.fastq.gz}2_001.fastq.gz \
        -p 8 -o ${f%R1_001.fastq.gz}_quant --validateMappings --gcBias & 
done
