#!/bin/bash
#Sampling to smallest library pair WT_IL4_replicate_I.bam containing9826554 reads
ln -s . mm9
echo WT_0h_replicate_I.bam
/data/results/tools/proton/tophat2unstranded-sampled-pair-bigwig1.sh WT_0h_replicate_I.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome  0.8904163415479798 WT_0h_replicate_II.bam
echo WT_2h_replicate_I.bam
/data/results/tools/proton/tophat2unstranded-sampled-pair-bigwig1.sh WT_2h_replicate_I.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome  1.0 WT_2h_replicate_II.bam
echo WT_IL4_replicate_I.bam
/data/results/tools/proton/tophat2unstranded-sampled-pair-bigwig1.sh WT_IL4_replicate_I.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9. 0.9487685201897585 WT_IL4_replicate_II.bam
echo WT_6h_replicate_I.bam
/data/results/tools/proton/tophat2unstranded-sampled-pair-bigwig1.sh WT_6h_replicate_I.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome  0.8434497816796398 WT_6h_replicate_II.bam
echo WT_IFN-gamma_replicate_I.bam
/data/results/tools/proton/tophat2unstranded-sampled-pair-bigwig1.sh WT_IFN-gamma_replicate_I.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome  0.7621949936732164 WT_IFN-gamma_replicate_II.bam
echo KO_0h_replicate_I.bam
/data/results/tools/proton/tophat2unstranded-sampled-pair-bigwig1.sh KO_0h_replicate_I.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome  0.809368877176937 KO_0h_replicate_II.bam
echo KO_2h_replicate_I.bam
/data/results/tools/proton/tophat2unstranded-sampled-pair-bigwig1.sh KO_2h_replicate_I.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome  0.5236029276455871 KO_2h_replicate_II.bam
echo KO_6h_replicate_I.bam
/data/results/tools/proton/tophat2unstranded-sampled-pair-bigwig1.sh KO_6h_replicate_I.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome  0.5005940785474009 KO_6h_replicate_II.bam
echo KO_IL4_replicate_I.bam
/data/results/tools/proton/tophat2unstranded-sampled-pair-bigwig1.sh KO_IL4_replicate_I.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome  0.6177434840786683 KO_IL4_replicate_II.bam
echo KO_IFN-gamma_replicate_I.bam
/data/results/tools/proton/tophat2unstranded-sampled-non-pair-bigwig1.sh KO_IFN_replicate_I.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome  0.5286996717314965 KO_IFN-gamma_replicate_II.bam