This is a simple program to automate star alignment and quantification using RSEM.
1.Download both the python file and shell script and store it in a folder. For example: if My fastq files are in the directory "fastq_files", i will download the two programs and store it in the "scripts" directory which is under "fastq_files" directory.
2.E.g. In my case, to pass the name of the fastq file i just need to add "../{filename}_R1.fastq".
3.Please put complete link to your star aligner and rsem when you execute the program.
4.Only star_alignment_and_rsem_automation.py file should be executed, the programs call and execute the shell script by itself.
Cheers!
Fill free to reach me for any suggestions or help also feel free to edit the code