#!/bin/bash

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/B1/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/B1-accepted_hits.bw;


cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/B2/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/B2-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/B3/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/B3-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/B4/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/B4-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/B5/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/B5-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/B6/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/B6-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/B7/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/B7-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/B8/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/B8-accepted_hits.bw;



cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/C1/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/C1-accepted_hits.bw;


cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/C2/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/C2-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/C3/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/C3-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/C4/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/C4-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/C5/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/C5-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/C6/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/C6-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/C7/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/C7-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/C8/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/C8-accepted_hits.bw;



cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/O1/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/O1-accepted_hits.bw;


cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/O2/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/O2-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/O3/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/O3-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/O4/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/O4-accepted_hits.bw;



cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/P1/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/P1-accepted_hits.bw;


cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/P2/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/P2-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/P3/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/P3-accepted_hits.bw;

cd /ddn/gs1/home/wangt4/IntegrativeBioinfo/Franco/Steve/Mm-PRA+PRB-RNAseq/P4/TopHat-Out;

genomeCoverageBed -ibam accepted_hits.bam -g ../mm10.chr.size -bg -split > accepted_hits.bedgraph;


bedGraphToBigWig accepted_hits.bedgraph ../mm10.chr.size accepted_hits.bw;
cp accepted_hits.bw /data/wade/DeMayo/Mouse-PRKO-RNAseq/P4-accepted_hits.bw;