I have very large RNA-seq files generated in different lanes. I extracted few of the file names as shown below.
MC9_FNEN_638A_S19_L008_R1_001.fastq.gz
MC9_FNEN_638A_S19_L008_R2_001.fastq.gz
MC9_FNEN_638A_S9_L001_R1_001.fastq.gz
MC9_FNEN_638A_S9_L001_R2_001.fastq.gz
MC9_FNEN_638A_S9_L002_R1_001.fastq.gz
MC9_FREN_638A_S9_L002_R2_001.fastq.gz
MC9_FREN_638A_S9_L006_R1_001.fastq.gz
MC9_FREN_638A_S9_L006_R2_001.fastq.gz
MC9_FREN_638A_S9_L008_R1_001.fastq.gz
MC9_FREN_638A_S9_L008_R2_001.fastq.gz
MC9_637A_S74_L001_R1_001.fastq.gz
MC9_ZH_637A_S74_L001_R2_001.fastq.gz
MC9_ZH_637A_S74_L003_R1_001.fastq.gz
MC9_ZH_637A_S74_L003_R2_001.fastq.gz
MC9_ZH_637A_S74_L007_R1_001.fastq.gz
MC9_ZH_637A_S74_L007_R2_001.fastq.gz
MC9_ZH_637A_S74_L008_R1_001.fastq.gz
MC9_ZH_637A_S74_L008_R2_001.fastq.gz
MC9_ZH_637A_S84_L008_R1_001.fastq.gz
MC9_ZH_637A_S84_L008_R2_001.fastq.gz
DR14_DCRP_479C_S50_L001_R1_001.fastq.gz
DR14_DCRP_479C_S50_L001_R2_001.fastq.gz
DR14_DCRP_479C_S50_L002_R1_001.fastq.gz
DR14_DCRP_479C_S50_L002_R2_001.fastq.gz
DR14_DCRP_479C_S50_L006_R1_001.fastq.gz
DR14_DCRP_479C_S50_L006_R2_001.fastq.gz
DR14_DCRP_479C_S50_L007_R1_001.fastq.gz
DR14_DCRP_479C_S50_L007_R2_001.fastq.gz
DR14_DCRP_479C_S50_L008_R1_001.fastq.gz
DR14_DCRP_479C_S50_L008_R2_001.fastq.gz
I want to concatenate all the sequence generated in different lanes for the forward and reverse read. For example the first 10 lines are sequence file from the same animal and specific tissue (`MC9_FREN`). I want to concatenate all the forward read `XXXXX_R1_001.fastq.gz` that are generated in different lanes and put in the file name `MC9_FREN_R1.fastq.gz` and all reverse reads `XXXX_R2_001.fastq.gz` to `MC9_FREN_R2.fastq.gz`
cat MC9_FREN_638A_S19_L008_R1_001.fastq.gz MC9_FREN_638A_S9_L001_R1_001.fastq.gz MC9_FREN_638A_S9_L002_R1_001.fastq.gz MC9_FREN_638A_S9_L007_R1_001.fastq.gz MC9_FREN_638A_S9_L008_R1_001.fastq.gz > MC9_FREN_R1.fastq.gz
cat MC9_FREN_638A_S19_L008_R2_001.fastq.gz MC9_FREN_638A_S9_L001_R2_001.fastq.gz MC9_FREN_638A_S9_L002_R2_001.fastq.gz MC9_FREN_638A_S9_L007_R2_001.fastq.gz MC9_FREN_638A_S9_L008_R2_001.fastq.gz > MC9_FREN_R2.fastq.gz
cat MC9_ZH_637A_S74_L001_R1_001.fastq.gz MC9_ZH_637A_S74_L003_R1_001.fastq.gz MC9_ZH_637A_S74_L007_R1_001.fastq.gz MC9_ZH_637A_S74_L008_R1_001.fastq.gz MC9_ZH_637A_S84_L008_R1_001.fastq.gz > MC9_ZH_R1.gz
cat MC9_ZH_637A_S74_L001_R2_001.fastq.gz MC9_ZH_637A_S74_L003_R2_001.fastq.gz MC9_ZH_637A_S74_L007_R2_001.fastq.gz MC9_ZH_637A_S74_L008_R2_001.fastq.gz MC9_ZH_637A_S84_L008_R2_001.fastq.gz > MC9_ZH_R2.gz
cat DR14_DCRP_479C_S50_L001_R1_001.fastq.gz DR14_DCRP_479C_S50_L002_R1_001.fastq.gz DR14_DCRP_479C_S50_L006_R1_001.fastq.gz DR14_DCRP_479C_S50_L007_R1_001.fastq.gz DR14_DCRP_479C_S50_L008_R1_001.fastq.gz > DR14_DCRP_R1.gz
cat DR14_DCRP_479C_S50_L001_R2_001.fastq.gz DR14_DCRP_479C_S50_L002_R2_001.fastq.gz DR14_DCRP_479C_S50_L006_R2_001.fastq.gz DR14_DCRP_479C_S50_L007_R2_001.fastq.gz DR14_DCRP_479C_S50_L008_R2_001.fastq.gz > DR14_DCRP_R1.gz
MC9_FNEN_638A_S19_L008_R1_001.fastq.gz
MC9_FNEN_638A_S19_L008_R2_001.fastq.gz
MC9_FNEN_638A_S9_L001_R1_001.fastq.gz
MC9_FNEN_638A_S9_L001_R2_001.fastq.gz
MC9_FNEN_638A_S9_L002_R1_001.fastq.gz
MC9_FREN_638A_S9_L002_R2_001.fastq.gz
MC9_FREN_638A_S9_L006_R1_001.fastq.gz
MC9_FREN_638A_S9_L006_R2_001.fastq.gz
MC9_FREN_638A_S9_L008_R1_001.fastq.gz
MC9_FREN_638A_S9_L008_R2_001.fastq.gz
MC9_637A_S74_L001_R1_001.fastq.gz
MC9_ZH_637A_S74_L001_R2_001.fastq.gz
MC9_ZH_637A_S74_L003_R1_001.fastq.gz
MC9_ZH_637A_S74_L003_R2_001.fastq.gz
MC9_ZH_637A_S74_L007_R1_001.fastq.gz
MC9_ZH_637A_S74_L007_R2_001.fastq.gz
MC9_ZH_637A_S74_L008_R1_001.fastq.gz
MC9_ZH_637A_S74_L008_R2_001.fastq.gz
MC9_ZH_637A_S84_L008_R1_001.fastq.gz
MC9_ZH_637A_S84_L008_R2_001.fastq.gz
DR14_DCRP_479C_S50_L001_R1_001.fastq.gz
DR14_DCRP_479C_S50_L001_R2_001.fastq.gz
DR14_DCRP_479C_S50_L002_R1_001.fastq.gz
DR14_DCRP_479C_S50_L002_R2_001.fastq.gz
DR14_DCRP_479C_S50_L006_R1_001.fastq.gz
DR14_DCRP_479C_S50_L006_R2_001.fastq.gz
DR14_DCRP_479C_S50_L007_R1_001.fastq.gz
DR14_DCRP_479C_S50_L007_R2_001.fastq.gz
DR14_DCRP_479C_S50_L008_R1_001.fastq.gz
DR14_DCRP_479C_S50_L008_R2_001.fastq.gz
I want to concatenate all the sequence generated in different lanes for the forward and reverse read. For example the first 10 lines are sequence file from the same animal and specific tissue (`MC9_FREN`). I want to concatenate all the forward read `XXXXX_R1_001.fastq.gz` that are generated in different lanes and put in the file name `MC9_FREN_R1.fastq.gz` and all reverse reads `XXXX_R2_001.fastq.gz` to `MC9_FREN_R2.fastq.gz`
cat MC9_FREN_638A_S19_L008_R1_001.fastq.gz MC9_FREN_638A_S9_L001_R1_001.fastq.gz MC9_FREN_638A_S9_L002_R1_001.fastq.gz MC9_FREN_638A_S9_L007_R1_001.fastq.gz MC9_FREN_638A_S9_L008_R1_001.fastq.gz > MC9_FREN_R1.fastq.gz
cat MC9_FREN_638A_S19_L008_R2_001.fastq.gz MC9_FREN_638A_S9_L001_R2_001.fastq.gz MC9_FREN_638A_S9_L002_R2_001.fastq.gz MC9_FREN_638A_S9_L007_R2_001.fastq.gz MC9_FREN_638A_S9_L008_R2_001.fastq.gz > MC9_FREN_R2.fastq.gz
cat MC9_ZH_637A_S74_L001_R1_001.fastq.gz MC9_ZH_637A_S74_L003_R1_001.fastq.gz MC9_ZH_637A_S74_L007_R1_001.fastq.gz MC9_ZH_637A_S74_L008_R1_001.fastq.gz MC9_ZH_637A_S84_L008_R1_001.fastq.gz > MC9_ZH_R1.gz
cat MC9_ZH_637A_S74_L001_R2_001.fastq.gz MC9_ZH_637A_S74_L003_R2_001.fastq.gz MC9_ZH_637A_S74_L007_R2_001.fastq.gz MC9_ZH_637A_S74_L008_R2_001.fastq.gz MC9_ZH_637A_S84_L008_R2_001.fastq.gz > MC9_ZH_R2.gz
cat DR14_DCRP_479C_S50_L001_R1_001.fastq.gz DR14_DCRP_479C_S50_L002_R1_001.fastq.gz DR14_DCRP_479C_S50_L006_R1_001.fastq.gz DR14_DCRP_479C_S50_L007_R1_001.fastq.gz DR14_DCRP_479C_S50_L008_R1_001.fastq.gz > DR14_DCRP_R1.gz
cat DR14_DCRP_479C_S50_L001_R2_001.fastq.gz DR14_DCRP_479C_S50_L002_R2_001.fastq.gz DR14_DCRP_479C_S50_L006_R2_001.fastq.gz DR14_DCRP_479C_S50_L007_R2_001.fastq.gz DR14_DCRP_479C_S50_L008_R2_001.fastq.gz > DR14_DCRP_R1.gz
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