Created my own RNA-Seq pipeline

[akropor2]

Hi everyone,
My lab has been analyzing quite a bit of RNA-Seq data so I decided to create a small pipeline for them using tophat-->cufflinks-->cuffmerge-->cuffdiff as seen in the Trapnell et al., 2014 paper. I'm not a trained bioinformatician and am mostly self-taught so please take the following code with a grain of salt. However, if you would like to use it please feel free to. If you have tips on how I could improve my code please let me know.
The github link is the following:
https://github.com/akok619/RNA-Seq_tuxedo
The Readme file contains more information.
Good luck and thanks for taking the time!

[jerryschen]

Nice job! Your bioinformatics skills are good

[gringer]

You don't need to uncompress fastq files to run tophat2. It might be worth looking at HISAT2, a faster replacement from the makers of Tophat.

[akropor2]

Thanks for the suggestion gringer!