STAR=/grid/dobin/home/dobin/STAR/Releases/STAR-2.7.7a/bin/Linux_x86_64/STAR 
genomeDir=/grid/dobin/home/castro/Projects/BICCN/Data/Human_Chimp_Gorilla/Chimp/SmartSeq_GenomeGen/
fastqDir=/grid/dobin/home/castro/Projects/BICCN/Data/Human_Chimp_Gorilla/Chimp/MTG_SSv4_chimpanzee/
listDir=/grid/dobin/home/castro/Projects/BICCN/Human_Chimp_Gorilla/DonorLists/Chimp/


for dd in `cd $listDir; ls *_L2-3-IT.txt`
do
    echo aa $dd
    echo ${dd%%txt}
done

--genomeDir 
--readFilesIn 
--readFilesCommand zcat --outSAMtype None --quantMode TranscriptomeSAM --runThreadN 4