#for i in bams/GM-tr-0h-a.bam
for i in *.bam
do
echo $i
/data/results/tools/proton/tophat2stranded-bigwig-GRCh37a.sh $i /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 
done