module load java/8u25
module load samtools/latest
java -jar /net/waterston/vol9/bam2wig.jar -w 1 -s 1 -t -o /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/unscaled.wig /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/Aligned.toGenome.out.bam
java -cp /nfs/waterston/tools3/LabManagement.jar org.rhwlab.LMS.RNASeq.merged.MergedID /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/unscaled.wig 2.507974 /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/tbx37repT4_1_2_Merged1.wig
/net/waterston/vol9/wigToBigWig -clip /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/tbx37repT4_1_2_Merged1.wig /net/waterston/vol9/ce11.chrom.sizes /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/tbx37repT4_1_2_Merged1.bw
/net/waterston/vol9/bigWigToBedGraph  /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/tbx37repT4_1_2_Merged1.bw  /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/tbx37repT4_1_2_Merged1.bedGraph
rm -f /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/unscaled.wig 
java -jar /net/waterston/vol9/bam2wig.jar -w 1 -s 1 -t -o /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/unscaled.wig /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/Aligned.toGenome.unique.bam
java -cp /nfs/waterston/tools3/LabManagement.jar org.rhwlab.LMS.RNASeq.merged.MergedID /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/unscaled.wig 2.976229 /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/tbx37repT4_1_2_Merged1.unique.wig
/net/waterston/vol9/wigToBigWig -clip /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/tbx37repT4_1_2_Merged1.unique.wig /net/waterston/vol9/ce11.chrom.sizes /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/tbx37repT4_1_2_Merged1.unique.bw
/net/waterston/vol9/bigWigToBedGraph  /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/tbx37repT4_1_2_Merged1.unique.bw  /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/tbx37repT4_1_2_Merged1.unique.bedGraph
rm -f /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/unscaled.wig 
ssh epic.gs.washington.edu mv /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/*.bw /net/waterston/vol9/RNASeq/adwarner/tbx37rep_DS1/tbx37repT4_1_2/Merged_1/*.bedGraph /data/www/site/waterston/html/FACS/ 
