RNA_seq

Scripts related to RNA sequencing, transcriptomics, and analysis of differential gene expression

Contains three directories:

• blacklight_pipeline
• diff_expression/
• transcriptome_analysis/

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How to get these scripts

Install and setup git

Then in a terminal window, "cd" into a relevant directory, and clone this repository into a new_destination_directory within that:

 git clone git://github.com/safay/RNA_seq/ new_destination_directory

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blacklight_pipeline/

de-novo assembly, annotation, and expression estimation in systems without a pre-existing reference

diff_expression/

analyze differential expression from files generated in the blacklight pipeline

transcriptome_analysis/

get N50, compare histograms from different transcriptomes