I read python basic codes and I am fimiliar with for loops, But not able to understand how to make a python programme to run hisat2 on multiple pair-end reads.
I want to run hisat2 mapping tool on mutiple pair end reads to map these on Genome.
I already have prepared genome index.
1)my input will be hisat2 location and genome index, pair-end read file 2) How should I give multiple hisat2 arguments and how to store sam file in a separate folder for each pair-end reads.
Can you help to make this python script ?
Location of hisat2: /home/yog/software/hisat2-2.0.4/hisat2 Location of genome index: data/Analysis/Radish_index Location of pair end files: /data/Analysis/mapped/ multiple pair end files like this: 216_5W_Ca1_R1.fq 216_5W_Ca1_R2.fq 218_5W_Ca1_R1.fq 218_5W_Ca1_R1.fq 216_5W_Co1_R1.fq 216_5W_Co1_R2.fq 218_5W_Co1_R1.fq 218_5W_Co1_R1.fq
Now I am running hisat2 on individual files by using this commonad:
/home/yog/software/hisat2-2.0.4/hisat2 -p 8 -x /data/Analysis/Radish_index --fr -1 /data/Analysis/mapped/216_5W_Ca1_R1.fq -2 /data/Analysis/mapped/216_5W_Ca1_R2.fq -S 216_5W_Ca1.sam