rnabioco/hl-collab repository overview

⁠hesselberth-clp1

⁠UCSC trackhub

Various tracks are available here: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=http://amc-sandbox.ucdenver.edu/User33/hesselberth/hub/hub.txt⁠

⁠project data

All data is available here on bodhi: /beevol/home/riemondy/Projects/hesselberth-clp1

Processed and summary data files are shared on dropbox (clp1-project).

A full copy of my local files, which includes the data files called in each markdown is also on dropbox (clp1-project/local-repo) (~70Gb).

⁠directory contents

⁠data

mostly empty, except for a few bash scripts used for processing the ribozyme libraries.

on bodhi contains all of the data produced by bespoke bash scripts or snakemake pipelines in the pipeline directory

⁠dbases

scripts for download various genome files on bodhi, includes star and salmon indexes and other databases used by the pipelines

⁠docker

contains the dockerfile for the docker image used by snakemake pipelines envoked with the --use-singularity flag.

Also used by the ribozyme processing bash scripts.

The docker image is available on dockerhub: https://hub.docker.com/repository/docker/rnabioco/hl-collab/general⁠ and a singularity image is already on bodhi (clp1-08-16-2024.sif).

⁠hub

contains all of the scripts and trackDb files for the trackhub, but none of the data. The data is all hosted at http://amc-sandbox.ucdenver.edu/User33/hesselberth/hub/⁠ and mirrored on bodhi at /beevol/home/riemondy/Projects/hesselberth-clp1/hub

⁠pipeline

Various snakemake pipelines for different libraries generate for the project.

⁠results

Rmarkdown and related analysis files for individual analyses. The html and output files are shared on dropbox (clp1-project)

⁠src

Various scripts used for the project including some early bash scripts used for pipelining some library processing.