#!/bin/bash

ln -s ../reads/tophat/KO_0h_replicate_Ib/accepted_hits.bam KO_0h_replicate_I.bam 
ln -s ../reads/tophat/KO_0h_replicate_IIb/accepted_hits.bam KO_0h_replicate_II.bam

ln -s ../reads/tophat/KO_2h_replicate_Ib/accepted_hits.bam  KO_2h_replicate_I.bam 
ln -s ../reads/tophat/KO_2h_replicate_IIb/accepted_hits.bam KO_2h_replicate_II.bam

ln -s ../reads/tophat/KO_6h_replicate_Ib/accepted_hits.bam  KO_6h_replicate_I.bam	  
ln -s ../reads/tophat/KO_6h_replicate_IIb/accepted_hits.bam   KO_6h_replicate_II.bam	

ln -s ../reads/tophat/KO_IFN-gamma_replicate_IIb/accepted_hits.bam KO_IFN-gamma_replicate_II.bam 
ln -s ../reads/tophat/KO_IFN_replicate_Ib/accepted_hits.bam         KO_IFN-gamma_replicate_I.bam

ln -s ../reads/tophat/KO_IL4_replicate_Ib/accepted_hits.bam  KO_IL4_replicate_I.bam   
ln -s ../reads/tophat/KO_IL4_replicate_IIb/accepted_hits.bam   KO_IL4_replicate_II.bam


ln -s ../reads/tophat/WT_0h_replicate_Ib/accepted_hits.bam  WT_0h_replicate_I.bam  
ln -s ../reads/tophat/WT_0h_replicate_IIb/accepted_hits.bam WT_0h_replicate_II_.bam

ln -s ../reads/tophat/WT_2h_replicate_Ib/accepted_hits.bam  WT_2h_replicate_I.bam 
ln -s ../reads/tophat/WT_2h_replicate_IIb/accepted_hits.bam WT_2h_replicate_II.bam

ln -s ../reads/tophat/WT_6h_replicate_Ib/accepted_hits.bam  WT_6h_replicate_I.bam 
ln -s ../reads/tophat/WT_6h_replicate_IIb/accepted_hits.bam WT_6h_replicate_II.bam

ln -s ../reads/tophat/WT_IFN-gamma_replicate_Ib/accepted_hits.bam  WT_IFN-gamma_replicate_I.bam 
ln -s ../reads/tophat/WT_IFN-gamma_replicate_IIb/accepted_hits.bam WT_IFN-gamma_replicate_II.bam

ln -s ../reads/tophat/WT_IL4_replicate_Ib/accepted_hits.bam  WT_IL4_replicate_I.bam 
ln -s ../reads/tophat/WT_IL4_replicate_IIb/accepted_hits.bam WT_IL4_replicate_II.bam