ln -s /data/images/proton2/run374/R_2017_12_07_15_50_07_user_IONAS-374-DrKobold_PHlab_YK_KELPNO_171207.SK3R1-Tbctrl2.IonXpress_033.fastq SK3R1-Tbctrl2.fastq
#/data/images/proton2/run374/tophat_033/sort_uniq.bam SK3R1-Tbctrl2.bam
ln -s /data/images/proton2/run374/R_2017_12_07_15_50_07_user_IONAS-374-DrKobold_PHlab_YK_KELPNO_171207.SK3R2-Tbctrl3.IonXpress_034.fastq SK3R2-Tbctrl3.fastq
#/data/images/proton2/run374/tophat_034/sort_uniq.bam SK3R2-Tbctrl3.bam
ln -s /data/images/proton2/run374/R_2017_12_07_15_50_07_user_IONAS-374-DrKobold_PHlab_YK_KELPNO_171207.SK3R3-Tbctrl4.IonXpress_035.fastq SK3R3-Tbctrl4.fastq
#/data/images/proton2/run374/tophat_035/sort_uniq.bam SK3R3-Tbctrl4.bam
ln -s /data/images/proton2/run373/R_2017_12_01_12_13_27_user_IONAS-373-DrKobold_PHlab_171201_SK3R-PH4C.SK3R10-Tdil22-9.IonXpress_010.fastq SK3R10-Tdil22-9b.fastq
#/data/images/proton2/run373/tophat_010/sort_uniq.bam SK3R10-Tdil22-9b.bam
ln -s /data/images/proton2/run373/R_2017_12_01_12_13_27_user_IONAS-373-DrKobold_PHlab_171201_SK3R-PH4C.SK3R11-Tdil22-10.IonXpress_011.fastq SK3R11-Tdil22-10b.fastq
#/data/images/proton2/run373/tophat_011/sort_uniq.bam SK3R11-Tdil22-10b.bam
ln -s /data/images/proton2/run373/R_2017_12_01_12_13_27_user_IONAS-373-DrKobold_PHlab_171201_SK3R-PH4C.SK3R12-Tdil22-11.IonXpress_012.fastq SK3R12-Tdil22-11b.fastq
#/data/images/proton2/run373/tophat_012/sort_uniq.bam SK3R12-Tdil22-11b.bam
ln -s /data/images/proton2/run373/R_2017_12_01_12_13_27_user_IONAS-373-DrKobold_PHlab_171201_SK3R-PH4C.SK3R16-Lbil22-7.IonXpress_016.fastq SK3R16-Lbil22-7b.fastq
#/data/images/proton2/run373/tophat_016/sort_uniq.bam SK3R16-Lbil22-7b.bam
ln -s /data/images/proton2/run373/R_2017_12_01_12_13_27_user_IONAS-373-DrKobold_PHlab_171201_SK3R-PH4C.SK3R18-Lbil22-9.IonXpress_018.fastq SK3R18-Lbil22-9b.fastq
#/data/images/proton2/run373/tophat_018/sort_uniq.bam SK3R18-Lbil22-9b.bam
ln -s /data/images/proton2/run373/R_2017_12_01_12_13_27_user_IONAS-373-DrKobold_PHlab_171201_SK3R-PH4C.SK3R19-Lcctrl3.IonXpress_019.fastq SK3R19-Lcctrl3b.fastq
#/data/images/proton2/run373/tophat_019/sort_uniq.bam SK3R19-Lcctrl3b.bam
ln -s /data/images/proton2/run373/R_2017_12_01_12_13_27_user_IONAS-373-DrKobold_PHlab_171201_SK3R-PH4C.SK3R4-Tbil22-7.IonXpress_004.fastq SK3R4-Tbil22-7b.fastq
#/data/images/proton2/run373/tophat_004/sort_uniq.bam SK3R4-Tbil22-7b.bam
ln -s /data/images/proton2/run373/R_2017_12_01_12_13_27_user_IONAS-373-DrKobold_PHlab_171201_SK3R-PH4C.SK3R6-Tbil22-12.IonXpress_006.fastq SK3R6-Tbil22-12b.fastq
#/data/images/proton2/run373/tophat_006/sort_uniq.bam SK3R6-Tbil22-12b.bam
ln -s /data/images/proton2/run371/R_2017_11_22_16_29_11_user_IONAS-371-DrKobold_171122_SK3R13-24.SK3R13-Lbctrl4.IonXpress_013.fastq SK3R13-Lbctrl4.fastq
#/data/images/proton2/run371/tophat_013/sort_uniq.bam SK3R13-Lbctrl4.bam
ln -s /data/images/proton2/run371/R_2017_11_22_16_29_11_user_IONAS-371-DrKobold_171122_SK3R13-24.SK3R14-Lbctrl5.IonXpress_014.fastq SK3R14-Lbctrl5.fastq
#/data/images/proton2/run371/tophat_014/sort_uniq.bam SK3R14-Lbctrl5.bam
ln -s /data/images/proton2/run371/R_2017_11_22_16_29_11_user_IONAS-371-DrKobold_171122_SK3R13-24.SK3R15-Lbctrl6.IonXpress_015.fastq SK3R15-Lbctrl6.fastq
#/data/images/proton2/run371/tophat_015/sort_uniq.bam SK3R15-Lbctrl6.bam
ln -s /data/images/proton2/run371/R_2017_11_22_16_29_11_user_IONAS-371-DrKobold_171122_SK3R13-24.SK3R16-Lbil22-7.IonXpress_016.fastq SK3R16-Lbil22-7.fastq
#/data/images/proton2/run371/tophat_016/sort_uniq.bam SK3R16-Lbil22-7.bam
ln -s /data/images/proton2/run371/R_2017_11_22_16_29_11_user_IONAS-371-DrKobold_171122_SK3R13-24.SK3R17-Lbil22-8.IonXpress_017.fastq SK3R17-Lbil22-8.fastq
#/data/images/proton2/run371/tophat_017/sort_uniq.bam SK3R17-Lbil22-8.bam
ln -s /data/images/proton2/run371/R_2017_11_22_16_29_11_user_IONAS-371-DrKobold_171122_SK3R13-24.SK3R18-Lbil22-9.IonXpress_018.fastq SK3R18-Lbil22-9.fastq
#/data/images/proton2/run371/tophat_018/sort_uniq.bam SK3R18-Lbil22-9.bam
ln -s /data/images/proton2/run371/R_2017_11_22_16_29_11_user_IONAS-371-DrKobold_171122_SK3R13-24.SK3R19-Lcctrl3.IonXpress_019.fastq SK3R19-Lcctrl3.fastq
#/data/images/proton2/run371/tophat_019/sort_uniq.bam SK3R19-Lcctrl3.bam
ln -s /data/images/proton2/run371/R_2017_11_22_16_29_11_user_IONAS-371-DrKobold_171122_SK3R13-24.SK3R20-Lcctrl4.IonXpress_020.fastq SK3R20-Lcctrl4.fastq
#/data/images/proton2/run371/tophat_020/sort_uniq.bam SK3R20-Lcctrl4.bam
ln -s /data/images/proton2/run371/R_2017_11_22_16_29_11_user_IONAS-371-DrKobold_171122_SK3R13-24.SK3R21-Lcctrl6.IonXpress_021.fastq SK3R21-Lcctrl6.fastq
#/data/images/proton2/run371/tophat_021/sort_uniq.bam SK3R21-Lcctrl6.bam
ln -s /data/images/proton2/run371/R_2017_11_22_16_29_11_user_IONAS-371-DrKobold_171122_SK3R13-24.SK3R22-Lcil22-8.IonXpress_022.fastq SK3R22-Lcil22-8.fastq
#/data/images/proton2/run371/tophat_022/sort_uniq.bam SK3R22-Lcil22-8.bam
ln -s /data/images/proton2/run371/R_2017_11_22_16_29_11_user_IONAS-371-DrKobold_171122_SK3R13-24.SK3R23-Lcil22-11.IonXpress_023.fastq SK3R23-Lcil22-11.fastq
#/data/images/proton2/run371/tophat_023/sort_uniq.bam SK3R23-Lcil22-11.bam
ln -s /data/images/proton2/run371/R_2017_11_22_16_29_11_user_IONAS-371-DrKobold_171122_SK3R13-24.SK3R24-Lcil22-12.IonXpress_024.fastq SK3R24-Lcil22-12.fastq
#/data/images/proton2/run371/tophat_024/sort_uniq.bam SK3R24-Lcil22-12.bam
ln -s /data/images/proton2/run370/R_2017_11_22_13_20_24_user_IONAS-370-DrKobold_171122_SK3R1-12.SK3R10-Tdil22-9.IonXpress_010.fastq SK3R10-Tdil22-9.fastq
#/data/images/proton2/run370/tophat_010/sort_uniq.bam SK3R10-Tdil22-9.bam
ln -s /data/images/proton2/run370/R_2017_11_22_13_20_24_user_IONAS-370-DrKobold_171122_SK3R1-12.SK3R11-Tdil22-10.IonXpress_011.fastq SK3R11-Tdil22-10.fastq
#/data/images/proton2/run370/tophat_011/sort_uniq.bam SK3R11-Tdil22-10.bam
ln -s /data/images/proton2/run370/R_2017_11_22_13_20_24_user_IONAS-370-DrKobold_171122_SK3R1-12.SK3R12-Tdil22-11.IonXpress_012.fastq SK3R12-Tdil22-11.fastq
#/data/images/proton2/run370/tophat_012/sort_uniq.bam SK3R12-Tdil22-11.bam
ln -s /data/images/proton2/run370/R_2017_11_22_13_20_24_user_IONAS-370-DrKobold_171122_SK3R1-12.SK3R4-Tbil22-7.IonXpress_004.fastq SK3R4-Tbil22-7.fastq
#/data/images/proton2/run370/tophat_004/sort_uniq.bam SK3R4-Tbil22-7.bam
ln -s /data/images/proton2/run370/R_2017_11_22_13_20_24_user_IONAS-370-DrKobold_171122_SK3R1-12.SK3R5-Tbil22-11.IonXpress_005.fastq SK3R5-Tbil22-11.fastq
#/data/images/proton2/run370/tophat_005/sort_uniq.bam SK3R5-Tbil22-11.bam
ln -s /data/images/proton2/run370/R_2017_11_22_13_20_24_user_IONAS-370-DrKobold_171122_SK3R1-12.SK3R6-Tbil22-12.IonXpress_006.fastq SK3R6-Tbil22-12.fastq
#/data/images/proton2/run370/tophat_006/sort_uniq.bam SK3R6-Tbil22-12.bam
ln -s /data/images/proton2/run370/R_2017_11_22_13_20_24_user_IONAS-370-DrKobold_171122_SK3R1-12.SK3R7-Tdctrl2.IonXpress_007.fastq SK3R7-Tdctrl2.fastq
#/data/images/proton2/run370/tophat_007/sort_uniq.bam SK3R7-Tdctrl2.bam
ln -s /data/images/proton2/run370/R_2017_11_22_13_20_24_user_IONAS-370-DrKobold_171122_SK3R1-12.SK3R8-Tdctrl3.IonXpress_008.fastq SK3R8-Tdctrl3.fastq
#/data/images/proton2/run370/tophat_008/sort_uniq.bam SK3R8-Tdctrl3.bam
ln -s /data/images/proton2/run370/R_2017_11_22_13_20_24_user_IONAS-370-DrKobold_171122_SK3R1-12.SK3R9-Tdctrl6.IonXpress_009.fastq SK3R9-Tdctrl6.fastq
#/data/images/proton2/run370/tophat_009/sort_uniq.bam SK3R9-Tdctrl6.bam

#note that the following physical replicates were merged
samtools merge SK3R4-Tbil22-7m.bam SK3R4-Tbil22-7.bam SK3R4-Tbil22-7b.bam
samtools merge SK3R6-Tbil22-12m.bam SK3R6-Tbil22-12.bam SK3R6-Tbil22-12b.bam
samtools merge SK3R11-Tdil22-10m.bam SK3R11-Tdil22-10.bam SK3R11-Tdil22-10b.bam
samtools merge SK3R10-Tdil22-9m.bam SK3R10-Tdil22-9.bam SK3R10-Tdil22-9b.bam
samtools merge SK3R12-Tdil22-11m.bam SK3R12-Tdil22-11.bam SK3R12-Tdil22-11b.bam
samtools merge SK3R16-Lbil22-7m.bam SK3R16-Lbil22-7.bam SK3R16-Lbil22-7b.bam
samtools merge SK3R18-Lbil22-9m.bam SK3R18-Lbil22-9.bam SK3R18-Lbil22-9b.bam
samtools merge SK3R19-Lcctrl3m.bam SK3R19-Lcctrl3.bam SK3R19-Lcctrl3b.bam