This Journal contains a variety of different code that is used to download, process, and analyze ribosome sequencing data.
Every subfolder in this folder contains a very similar set of scripts that are used to to download and process ribosome profiling data and RNA sequencing data from either flies, mice, or E.coli. The description of what each individual step does and how these scripts should be run can be found on the updated intro to bioinformatics google docs.
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Final output. This folder contains an example of the final output you will see if you decide to run the read alignments through the RiboDiff package in order to analyze the differential expression between the control and treatment groups.
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Scripts. This folder contains all of the BASH scripts and command lists necessary to run the alignments. Note that these scripts are designed to be run on Compute Canada servers.
This folder contains a variety of scripts that attempted different methods of detecting elongation limitation. All of these methods were unsuccesful but I decided to keep them around just in case any of them become useful.
This folder contains a script that is used to compare the mean KS statistic for a set of EFP target genes and a set of Fmr1 target genes.