merging fastq

cd Sample_AS-DKO-CD4T_a-CD3CD28
cat AS-DKO-LCD3_AGGTTCAT_L002_R1_001.fastq.gz AS-DKO-LCD3_AGGTTCAT_L002_R1_002.fastq.gz AS-DKO-LCD3_AGGTTCAT_L002_R1_003.fastq.gz AS-DKO-LCD3_AGGTTCAT_L002_R1_004.fastq.gz AS-DKO-LCD3_AGGTTCAT_L002_R1_005.fastq.gz AS-DKO-LCD3_AGGTTCAT_L002_R1_006.fastq.gz > tempR1.gz
cat AS-DKO-LCD3_AGGTTCAT_L002_R2_001.fastq.gz AS-DKO-LCD3_AGGTTCAT_L002_R2_002.fastq.gz AS-DKO-LCD3_AGGTTCAT_L002_R2_003.fastq.gz AS-DKO-LCD3_AGGTTCAT_L002_R2_004.fastq.gz AS-DKO-LCD3_AGGTTCAT_L002_R2_005.fastq.gz AS-DKO-LCD3_AGGTTCAT_L002_R2_006.fastq.gz > tempR2.gz
rm *.fastq.gz
mv tempR1.gz AS-DKO-LCD3_AGGTTCAT_L002_R1_001.fastq.gz
mv tempR2.gz AS-DKO-LCD3_AGGTTCAT_L002_R2_001.fastq.gz
cd ..

cd Sample_AS-DKO-CD4T_P+I
cat AS-DKO-CD4T_ATATAAGA_L002_R1_001.fastq.gz AS-DKO-CD4T_ATATAAGA_L002_R1_002.fastq.gz AS-DKO-CD4T_ATATAAGA_L002_R1_003.fastq.gz AS-DKO-CD4T_ATATAAGA_L002_R1_004.fastq.gz AS-DKO-CD4T_ATATAAGA_L002_R1_005.fastq.gz AS-DKO-CD4T_ATATAAGA_L002_R1_006.fastq.gz > tempR1.gz
cat AS-DKO-CD4T_ATATAAGA_L002_R2_001.fastq.gz AS-DKO-CD4T_ATATAAGA_L002_R2_002.fastq.gz AS-DKO-CD4T_ATATAAGA_L002_R2_003.fastq.gz AS-DKO-CD4T_ATATAAGA_L002_R2_004.fastq.gz AS-DKO-CD4T_ATATAAGA_L002_R2_005.fastq.gz AS-DKO-CD4T_ATATAAGA_L002_R2_006.fastq.gz > tempR2.gz
rm *.fastq.gz
mv tempR1.gz AS-DKO-CD4T_ATATAAGA_L002_R1_001.fastq.gz
mv tempR2.gz AS-DKO-CD4T_ATATAAGA_L002_R2_001.fastq.gz
cd ..

cd Sample_AS-WT-CD4T_a-CD3CD28
cat AS-WT-LCD3_AGCGCTGG_L002_R1_001.fastq.gz AS-WT-LCD3_AGCGCTGG_L002_R1_002.fastq.gz AS-WT-LCD3_AGCGCTGG_L002_R1_003.fastq.gz AS-WT-LCD3_AGCGCTGG_L002_R1_004.fastq.gz AS-WT-LCD3_AGCGCTGG_L002_R1_005.fastq.gz > tempR1.gz
cat AS-WT-LCD3_AGCGCTGG_L002_R2_001.fastq.gz AS-WT-LCD3_AGCGCTGG_L002_R2_002.fastq.gz AS-WT-LCD3_AGCGCTGG_L002_R2_003.fastq.gz AS-WT-LCD3_AGCGCTGG_L002_R2_004.fastq.gz AS-WT-LCD3_AGCGCTGG_L002_R2_005.fastq.gz > tempR2.gz
rm *.fastq.gz
mv tempR1.gz AS-WT-LCD3_AGCGCTGG_L002_R1_001.fastq.gz
mv tempR2.gz AS-WT-LCD3_AGCGCTGG_L002_R2_001.fastq.gz
cd ..

cd Sample_AS-WT-CD4T_P+I
cat AS-WT-CD4T_AGTTATAG_L002_R1_001.fastq.gz AS-WT-CD4T_AGTTATAG_L002_R1_002.fastq.gz AS-WT-CD4T_AGTTATAG_L002_R1_003.fastq.gz AS-WT-CD4T_AGTTATAG_L002_R1_004.fastq.gz AS-WT-CD4T_AGTTATAG_L002_R1_005.fastq.gz > tempR1.gz
cat AS-WT-CD4T_AGTTATAG_L002_R2_001.fastq.gz AS-WT-CD4T_AGTTATAG_L002_R2_002.fastq.gz AS-WT-CD4T_AGTTATAG_L002_R2_003.fastq.gz AS-WT-CD4T_AGTTATAG_L002_R2_004.fastq.gz AS-WT-CD4T_AGTTATAG_L002_R2_005.fastq.gz > tempR2.gz
rm *.fastq.gz
mv tempR1.gz AS-WT-CD4T_AGTTATAG_L002_R1_001.fastq.gz
mv tempR2.gz AS-WT-CD4T_AGTTATAG_L002_R2_001.fastq.gz
cd ..