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  • Created my own RNA-Seq pipeline

    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!

  • #2
    Nice job! Your bioinformatics skills are good

    Comment


    • #3
      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.

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      • #4
        Thanks for the suggestion gringer!

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