RNA seq

Question

[rishav513]

I need help in writing a python code to automate the pipeline between two packages of RNA seq data as data output passed from bowtie will automatically become one of the input in tophat then output of tophat as input to cufflinks software as I am new to Python, I have experience only in R. So, I do not know how to do this.

Someone, please help.

[brunobsouzaa]

You can easily do this in bash instead of python. Suppose that you have your fastq files in one single folder, you can do something like:

for i in $(ls *.fastq.gz | uniq);
do
bowtie input=${i} output=${i}.out &&
tophat input=${i}.out output=${i}.tophat.out
done;

Of course, that's just a small suggestion... Just write the proper code for your needs.

Hope it helps!

[rishav513]

Thank you for your valuable suggestion.

[Ram]

It should be ${i} (the variable), not $(i) which is executing a subshell.

[brunobsouzaa]

You're right... Thanks for pointing this out!