#!/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 24443218
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR22-IgGRiPC57-1M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR23r-IgGRiPC57-2M.bam 36101320
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR23r-IgGRiPC57-2M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR24r-IgGRiPC57-3F.bam 40916907
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR24r-IgGRiPC57-3F.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR9-InputTg6105-3F.bam 29810178
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR9-InputTg6105-3F.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR19-HuRRiPC57-1M.bam 30817781
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR19-HuRRiPC57-1M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR21-HuRRiPC57-3F.bam 36514726
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR21-HuRRiPC57-3F.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR10-InputC57-1M.bam 32817593
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR10-InputC57-1M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR11-InputC57-2M.bam 30585825
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR11-InputC57-2M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR12-InputC57-3F.bam 36592882
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR12-InputC57-3F.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR16_M2RiPTg6105-1M.bam 30354692
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR16_M2RiPTg6105-1M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR17r_M2RiPTg6105-2M.bam 35026604
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR17r_M2RiPTg6105-2M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR18_M2RiPTg6105-3F.bam 28671794
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR18_M2RiPTg6105-3F.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR13r_M2RiPWt-1M.bam 20739179
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR13r_M2RiPWt-1M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR14r_M2RiPWt-2M.bam 35527719
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR14r_M2RiPWt-2M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR15r_M2RiPWt-3F.bam 40893185
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR15r_M2RiPWt-3F.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR5_InputWt-2M.bam 24144858
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR5_InputWt-2M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR6_InputWt-3F.bam 22475253
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR6_InputWt-3F.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR7_InputTg6105-1M.bam 22008974
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR7_InputTg6105-1M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai
echo DKR8_InputTg6105-2M.bam 21593941
/data/results/tools/proton/tophat2unstranded-bigwig1.sh DKR8_InputTg6105-2M.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai