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concatenate_shallow_deep_HiChIP_fastqs.sh
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#28
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_28/ams_28_EKDL220000677-1a_HY5VMDSX2_L4_1.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_28/ams_28_EKDL220000677-1a_HGCLFDSX3_L2_1.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_28/ams_28_EKDL220000677-1a_HK5H3DSX3_L3_1.fq.gz \
> E14_D4_TKO_H3K27ac_HiChIP_AMS052022_rep2_R1.fastq.gz
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_28/ams_28_EKDL220000677-1a_HY5VMDSX2_L4_2.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_28/ams_28_EKDL220000677-1a_HGCLFDSX3_L2_2.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_28/ams_28_EKDL220000677-1a_HK5H3DSX3_L3_2.fq.gz \
> E14_D4_TKO_H3K27ac_HiChIP_AMS052022_rep2_R2.fastq.gz
#27
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_27/ams_27_EKDL220000676-1a_HY5VMDSX2_L4_1.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_27/ams_27_EKDL220000676-1a_HGCLFDSX3_L2_1.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_27/ams_27_EKDL220000676-1a_HJW25DSX3_L2_1.fq.gz \
> E14_D4_TKO_H3K27ac_HiChIP_AMS052022_rep1_R1.fastq.gz
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_27/ams_27_EKDL220000676-1a_HY5VMDSX2_L4_2.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_27/ams_27_EKDL220000676-1a_HGCLFDSX3_L2_2.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_27/ams_27_EKDL220000676-1a_HJW25DSX3_L2_2.fq.gz \
> E14_D4_TKO_H3K27ac_HiChIP_AMS052022_rep1_R2.fastq.gz
#26
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_26/ams_26_EKDL220000675-1a_HY5VMDSX2_L4_1.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_26/ams_26_EKDL220000675-1a_HGCLFDSX3_L2_1.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_26/ams_26_EKDL220000675-1a_HJW25DSX3_L2_1.fq.gz \
> E14_D4_WT_H3K27ac_HiChIP_AMS052022_rep2_R1.fastq.gz
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_26/ams_26_EKDL220000675-1a_HY5VMDSX2_L4_2.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_26/ams_26_EKDL220000675-1a_HGCLFDSX3_L2_2.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_26/ams_26_EKDL220000675-1a_HJW25DSX3_L2_2.fq.gz \
> E14_D4_WT_H3K27ac_HiChIP_AMS052022_rep2_R2.fastq.gz
#25
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_25/ams_25_EKDL220000674-1a_HY5VMDSX2_L4_1.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_25/ams_25_EKDL220000674-1a_HGCLFDSX3_L2_1.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_25/ams_25_EKDL220000674-1a_HK5H3DSX3_L3_1.fq.gz \
> E14_D4_WT_H3K27ac_HiChIP_AMS052022_rep1_R1.fastq.gz
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_25/ams_25_EKDL220000674-1a_HY5VMDSX2_L4_2.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_25/ams_25_EKDL220000674-1a_HGCLFDSX3_L2_2.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_25/ams_25_EKDL220000674-1a_HK5H3DSX3_L3_2.fq.gz \
> E14_D4_WT_H3K27ac_HiChIP_AMS052022_rep1_R2.fastq.gz
#24
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_24/ams_24_EKDL220000673-1a_HY5VMDSX2_L4_1.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_24/ams_24_EKDL220000673-1a_HGCFMDSX3_L3_1.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_24/ams_24_EKDL220000673-1a_HGCLFDSX3_L2_1.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_24/ams_24_EKDL220000673-1a_HK5H3DSX3_L3_1.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_24/ams_24_EKDL220000673-1a_HK7WYDSX3_L2_1.fq.gz \
> E14_D0_TKO_H3K27ac_HiChIP_AMS052022_rep2_R1.fastq.gz
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_24/ams_24_EKDL220000673-1a_HY5VMDSX2_L4_2.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_24/ams_24_EKDL220000673-1a_HGCFMDSX3_L3_2.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_24/ams_24_EKDL220000673-1a_HGCLFDSX3_L2_2.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_24/ams_24_EKDL220000673-1a_HK5H3DSX3_L3_2.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_24/ams_24_EKDL220000673-1a_HK7WYDSX3_L2_2.fq.gz \
> E14_D0_TKO_H3K27ac_HiChIP_AMS052022_rep2_R2.fastq.gz
#23
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_23/ams_23_EKDL220000672-1a_HY5VMDSX2_L4_1.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_23/ams_23_EKDL220000672-1a_HGCLFDSX3_L2_1.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_23/ams_23_EKDL220000672-1a_HK5H3DSX3_L2_1.fq.gz \
> E14_D0_TKO_H3K27ac_HiChIP_AMS052022_rep1_R1.fastq.gz
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_23/ams_23_EKDL220000672-1a_HY5VMDSX2_L4_2.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_23/ams_23_EKDL220000672-1a_HGCLFDSX3_L2_2.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_23/ams_23_EKDL220000672-1a_HK5H3DSX3_L2_2.fq.gz \
> E14_D0_TKO_H3K27ac_HiChIP_AMS052022_rep1_R2.fastq.gz
#22
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_22/ams_22_EKDL220000671-1a_HY5VMDSX2_L4_1.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_22/ams_22_EKDL220000671-1a_HGCLFDSX3_L2_1.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_22/ams_22_EKDL220000671-1a_HK5H3DSX3_L3_1.fq.gz \
> E14_D0_WT_H3K27ac_HiChIP_AMS052022_rep2_R1.fastq.gz
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_22/ams_22_EKDL220000671-1a_HY5VMDSX2_L4_2.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_22/ams_22_EKDL220000671-1a_HGCLFDSX3_L2_2.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_22/ams_22_EKDL220000671-1a_HK5H3DSX3_L3_2.fq.gz \
> E14_D0_WT_H3K27ac_HiChIP_AMS052022_rep2_R2.fastq.gz
#21
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_21/ams_21_EKDL220000670-1a_HY5VMDSX2_L4_1.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_21/ams_21_EKDL220000670-1a_HGCFMDSX3_L3_1.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_21/ams_21_EKDL220000670-1a_HGCLFDSX3_L2_1.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_21/ams_21_EKDL220000670-1a_HK5H3DSX3_L2_1.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_21/ams_21_EKDL220000670-1a_HK7WYDSX3_L2_1.fq.gz \
> E14_D0_WT_H3K27ac_HiChIP_AMS052022_rep1_R1.fastq.gz
cat 2022_02_HiCHIP_shallow_AMS/X204SC22012716-Z01-F001/raw_data/ams_21/ams_21_EKDL220000670-1a_HY5VMDSX2_L4_2.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_21/ams_21_EKDL220000670-1a_HGCFMDSX3_L3_2.fq.gz \
2022_03_HiCHIP_intermediate_AMS/X204SC22032275-Z01-F001/raw_data/ams_21/ams_21_EKDL220000670-1a_HGCLFDSX3_L2_2.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_21/ams_21_EKDL220000670-1a_HK5H3DSX3_L2_2.fq.gz \
2022_05_HiCHIP_deep_AMS/raw_data/ams_21/ams_21_EKDL220000670-1a_HK7WYDSX3_L2_2.fq.gz \
> E14_D0_WT_H3K27ac_HiChIP_AMS052022_rep1_R2.fastq.gz