export SHRIMP_FOLDER=/data/results/tools/align/SHRiMP_2_2_3

#max
./shrimp-map-ncRNA1.sh1  &> shrimp-map-ncRNA1.sh1.log &
#fix (avoid tmp bam file clashes)
cd b
./shrimp-map-ncRNA1.sh2  &> shrimp-map-ncRNA1.sh2.log &
mv b/* .


for i in *Mm.bam	 
do
    echo $i
    # add MD flags for bowtie format
    /data/results/tools/samtools/samtools-1.3/samtools calmd -b $i /data/results/reference/mmu/mm9/mRNA-genomic/mm9-genomic-mRNA.fa  >& /dev/null > foo.bam2
    samtools view -h foo.bam2  | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/sam2bowtie.awk  > $i.md.bt
    mv foo.bam2 $i.md.bam
done
cd /data/results/reference/mmu/mm9/ncRNA/
/home/reczko/bin/faToTwoBit mm9-ncRNA.fa mm9-ncRNA.2bit
#ini file:
/data/results/reference/mmu/mm9/ncRNA/mm9-ncRNA.2bit