for i in *bam
do
	 l=$(echo $i|cut -d'.' -f 1)
	 echo $l

samtools reheader /data/images/proton/run139/run139/sam.head $i  > bam2
/data/results/tools/samtools/mysamtools-0.1.19/samtools sort -@ 8 bam2 sorted.bam2
mv sorted.bam2.bam $l.bam2
rm bam2


#/data/results/tools/align/cufflinks-2.2.1.Linux_x86_64/cufflinks --no-length-correction --no-effective-length-correction -G /data/results/reference/mmu/mm10/Mus_musculus.GRCm38.84.last500nt.gtf -L $l --no-update-check --library-type fr-secondstrand --num-threads 10 -q -o $l/accepted_hits $l.bam2 &> $l.log
#	 /data/results/tools/align/cufflinks-2.2.1.Linux_x86_64/cufflinks --no-length-correction -G /data/results/reference/mmu/mm10/Mus_musculus.GRCm38.84.last500nt.gtf -L $l --no-update-check --library-type fr-secondstrand --num-threads 10 -q -o $l/accepted_hits1 $l.bam2 &> $l.log
	 /data/results/tools/align/cufflinks-2.2.1.Linux_x86_64/cufflinks --no-length-correction -g /data/results/reference/mmu/mm10/Mus_musculus.GRCm38.84.last500nt.gtf -L $l --no-update-check --library-type fr-secondstrand --num-threads 10 -q -o $l/accepted_hits $l.bam2 &> $l.log
done