#!/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 0.582764 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 0.66111 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.genome 1 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 0.878045 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 0.832457 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 0.762027 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 0.666669 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 0.677403 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 0.943057 KO_IL4_replicate_II.bam
echo KO_IFN-gamma_replicate_I.bam
#/data/results/tools/proton/tophat2unstranded-sampled-non-pair-bigwig1.sh KO_IFN-gamma_replicate_II.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.653574 KO_IFN-gamma_replicate_II.bam
/data/results/tools/proton/tophat2unstranded-sampled-non-pair-bigwig1.sh KO_IFN-gamma_replicate_I.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome 0.653574 KO_IFN-gamma_replicate_II.bam
echo KO_IFN_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 0.431923 KO_IFN_replicate_I.bam