Last updated: 2019-09-16

Checks: 1 1

Knit directory: cheRNA_pilot/analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.4.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: uncommitted changes

The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Repository version: 68df993

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  analysis/20190909_Count3ssRatioExample.Rmd
    Untracked:  docs/figure/20190909_Count3ssRatioExample.Rmd/

Unstaged changes:
    Modified:   analysis/20190805_PlotIntronPositions.Rmd
    Modified:   analysis/index.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
Rmd de62ab7 Benjmain Fair 2019-08-13 Start workflowr project.

Here I will analyze chromatin associated RNA-seq datasets for 5 LCL lines, prepped by Staley lab. Alongside these new dataests, I will also look at some published datasets for the same lines for RNA-seq ,4sU-RNA-seq (30min, 60min), as well as the chromatin associated RNA and soluble nuclear RNA from Werner et al, and some RNA-seq datasets using different fractions and rRNA deplete vs poly-A selection from Sultan et al.

All fastq files were trimmed to 50bp and aligned to hg38 with enzembl annotations in two-pass mode with STAR, with mostly default parameters.

Analysis of intron positions and general quantifications of splicing: How do the different datasets differ with where in the gene the splice sites are.

Analysis of cotranscriptional splicing by 3’ss ratio: Quantification of cotranscriptional splicing by comparing amount of splicing (as quantified by coverage before and after 3’ss) in nascent RNA-seq (chromatin associatied) versus standard RNA-seq.