Merge fastq I1 I2 R1 R2 reads into R1 and R2¶
usage: fastq_merge_RI.py [-h] -o1 O1 -o2 O2 -r1 R1 -r2 R2 -i1 I1 -i2 I2
optional arguments:
-h, --help show this help message and exit
-o1 O1 output R1 fastq file name (default: None)
-o2 O2 output R2 fastq file name (default: None)
-r1 R1 read1 fastq (default: None)
-r2 R2 read2 fastq (default: None)
-i1 I1 index1 fastq (default: None)
-i2 I2 index2 fastq (default: None)
Summary¶
Add I1 and I2 into R1 and R2. So the output fastq is like:
@VH00889:7:AACKJGLM5:1:1101:18269:1000 1:N:0:ACAGTGAT+AGATCTCG
AGGAATAGCATTAAATCTGCAGATAGCTTTGGGCAGTATGATCATTTTCA
+
CCCCCCCCCCCC;CCCCCCCCCCCCCCC--CCCCCC;CCCCCCCCCCCCC
Input¶
You need to specify I1, I2, R1 and R2 fastq file.
Output¶
You need to specify the output R1 and R2 fastq file name.
Usage¶
hpcf_interactive.sh
module load python/2.7.13
fastq_merge_RI.py -r1 2544979_GM_RNA1_S6_L001_R1_001.fastq.gz -r2 2544979_GM_RNA1_S6_L001_R3_001.fastq.gz -i1 2544979_GM_RNA1_S6_L001_I1_001.fastq.gz -i2 2544979_GM_RNA1_S6_L001_R2_001.fastq.gz -o1 GM_RNA1_S6_R1.fastq.gz -o2 GM_RNA1_S6_R2.fastq.gz