#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
#Sampling to smallest library containing2050808 reads
ln -s . mm10
echo SK3R10-Tdil22-9m.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R10-Tdil22-9m.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.50622
echo SK3R11-Tdil22-10m.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R11-Tdil22-10m.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.704814
echo SK3R12-Tdil22-11m.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R12-Tdil22-11m.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.688401
echo SK3R13-Lbctrl4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R13-Lbctrl4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.460905
echo SK3R14-Lbctrl5.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R14-Lbctrl5.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.485293
echo SK3R15-Lbctrl6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R15-Lbctrl6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.330018
echo SK3R16-Lbil22-7m.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R16-Lbil22-7m.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 1
echo SK3R17-Lbil22-8.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R17-Lbil22-8.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.475198
echo SK3R18-Lbil22-9m.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R18-Lbil22-9m.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.997923
echo SK3R19-Lcctrl3m.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R19-Lcctrl3m.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.880826
echo SK3R1-Tbctrl2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R1-Tbctrl2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.197903
echo SK3R20-Lcctrl4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R20-Lcctrl4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.645185
echo SK3R21-Lcctrl6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R21-Lcctrl6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.456446
echo SK3R22-Lcil22-8.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R22-Lcil22-8.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.488936
echo SK3R23-Lcil22-11.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R23-Lcil22-11.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.637188
echo SK3R24-Lcil22-12.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R24-Lcil22-12.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.50555
echo SK3R2-Tbctrl3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R2-Tbctrl3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.516259
echo SK3R3-Tbctrl4.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R3-Tbctrl4.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.533509
echo SK3R4-Tbil22-7m.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R4-Tbil22-7m.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.876835
echo SK3R5-Tbil22-11.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R5-Tbil22-11.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.681524
echo SK3R6-Tbil22-12m.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R6-Tbil22-12m.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.712881
echo SK3R7-Tdctrl2.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R7-Tdctrl2.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.709097
echo SK3R8-Tdctrl3.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R8-Tdctrl3.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.709753
echo SK3R9-Tdctrl6.bam
/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh SK3R9-Tdctrl6.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.mm10.fai 0.655802