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RNA-Seq: GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Newsbot! Literature Watch 0 10-15-2011 03:11 AM

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Old 11-05-2015, 10:30 AM   #1
akropor2
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Location: Wisconsin

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Smile 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!
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Old 11-05-2015, 02:20 PM   #2
jerryschen
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Nice job! Your bioinformatics skills are good
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Old 11-05-2015, 10:55 PM   #3
gringer
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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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Old 11-06-2015, 07:33 AM   #4
akropor2
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Thanks for the suggestion gringer!
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