#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing20739179 reads
ln -s . mm10
echo DKR22-IgGRiPC57-1M.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR22-IgGRiPC57-1M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.848464
echo DKR23r-IgGRiPC57-2M.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR23r-IgGRiPC57-2M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.574471
echo DKR24r-IgGRiPC57-3F.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR24r-IgGRiPC57-3F.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.506861
echo DKR9-InputTg6105-3F.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR9-InputTg6105-3F.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.695708
echo DKR19-HuRRiPC57-1M.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR19-HuRRiPC57-1M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.672961
echo DKR21-HuRRiPC57-3F.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR21-HuRRiPC57-3F.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.567968
echo DKR10-InputC57-1M.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR10-InputC57-1M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.631953
echo DKR11-InputC57-2M.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR11-InputC57-2M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.678065
echo DKR12-InputC57-3F.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR12-InputC57-3F.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.566754
echo DKR16_M2RiPTg6105-1M.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR16_M2RiPTg6105-1M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.683228
echo DKR17r_M2RiPTg6105-2M.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR17r_M2RiPTg6105-2M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.592098
echo DKR18_M2RiPTg6105-3F.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR18_M2RiPTg6105-3F.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.72333
echo DKR13r_M2RiPWt-1M.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR13r_M2RiPWt-1M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1
echo DKR14r_M2RiPWt-2M.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR14r_M2RiPWt-2M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.583746
echo DKR15r_M2RiPWt-3F.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR15r_M2RiPWt-3F.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.507155
echo DKR5_InputWt-2M.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR5_InputWt-2M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.858948
echo DKR6_InputWt-3F.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR6_InputWt-3F.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.922756
echo DKR7_InputTg6105-1M.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR7_InputTg6105-1M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.942306
echo DKR8_InputTg6105-2M.bam
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh DKR8_InputTg6105-2M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 0.960417