#!/bin/bash

PATH=/data/results/tools/align/cufflinks-2.2.1.Linux_x86_64:$PATH; export PATH

LABELS[1]="GKR13-wt1early"
LABELS[2]="GKR3-wt2early"
LABELS[3]="GKR5-wt3early"
LABELS[4]="GKR7-wt1late"
LABELS[5]="GKR9-wt2late"
LABELS[6]="GKR11-wt3late"
LABELS[7]="GKR2-DARE1early"
LABELS[8]="GKR4-DARE2early"
LABELS[9]="GKR6-DARE3early"
LABELS[10]="GKR8-DARE1late"
LABELS[11]="GKR10-DARE2late"
LABELS[12]="GKR12-DARE3late"

#ls G*/accepted_hits/transcripts.gtf > assemblies.txt
#/data/results/tools/align/cufflinks-2.2.1.Linux_x86_64/cuffmerge   -p 8 -s /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -o merged_asm -g /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Archives/archive-2013-03-06-15-01-24/Genes/genes.gtf  assemblies.txt



#BASE_DIR=/home/dimopoulos/TopHat_test/

#rm time_Cuff-mm9.txt
CONCUR=1
THREADS=8

i=4
j=5
k=6
l=10
m=11
n=12

echo ${LABELS[i]},${LABELS[j]},${LABELS[k]}
echo ${LABELS[l]},${LABELS[m]},${LABELS[n]}
cuffdiff -L ${LABELS[i]},${LABELS[l]} --no-effective-length-correction --library-type fr-secondstrand --no-update-check --num-threads $THREADS -q -o cuffdiff_${LABELS[i]}_vs_${LABELS[l]}  merged_asm/merged.gtf www/${LABELS[$i]}.bam,www/${LABELS[$j]}.bam,www/${LABELS[$k]}.bam www/${LABELS[$l]}.bam,www/${LABELS[$m]}.bam,www/${LABELS[$n]}.bam  &> cuffdiff_${LABELS[i]}_vs_${LABELS[l]}.log
exit