cd /data/images/proton/DKlab/orsalia2/stringtie
cp /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf .

remove yellow  in ~/bak/doc/fleming/kafasla/mapkap1/mails.txt
from
/data/images/proton/DKlab/orsalia2/stringtie/mapkap1-alt-splice-expressions.csv
gives: /data/images/proton/DKlab/orsalia2/stringtie/mapkap1-remove-transcripts-for-yellow-selection.txt
and /data/images/proton/DKlab/orsalia2/stringtie/mapkap1-remove-transcripts-for-white-selection.txt

remove those in 
gives: /data/images/proton/DKlab/orsalia2/stringtie/Mus_musculus.NCBIM37.64-toMM9-yellow.gtf
gives: /data/images/proton/DKlab/orsalia2/stringtie/Mus_musculus.NCBIM37.64-toMM9-white.gtf

/data/images/proton/DKlab/orsalia2/stringtie/runStringtie2.sh

/data/images/proton/DKlab/orsalia2/stringtie/runStringtie3.sh