https://github.com/kdm9/degradomeanalyser

A post-processing analysis toolkit for integrative degradomics
https://github.com/kdm9/degradomeanalyser

Last synced: 11 days ago
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A post-processing analysis toolkit for integrative degradomics

• Host: GitHub
• URL: https://github.com/kdm9/degradomeanalyser
• Owner: kdm9
• Created: 2012-10-31T05:15:16.000Z (about 12 years ago)
• Default Branch: master
• Last Pushed: 2013-06-21T06:14:24.000Z (over 11 years ago)
• Last Synced: 2024-10-11T19:22:58.907Z (about 1 month ago)
• Language: R
• Homepage:
• Size: 251 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
DegradomeAnalyseR:

=======

DegradomeAnalyseR is copyright 2012 Kevin Murray, and is licensed under the GPLv3 License.  

See http://www.gnu.org/licenses/gpl-3.0.txt for the full license text

USAGE:

======

These scripts are used in a bash pipeline, e.g.:

    - scrips/sanitise_paresnip_output.py  > 

    - paresnip/paresnip_filter.R --args  [  ... ] 

    - paresnip/paresnip_summarise.R --args  

    - rnaseq/paresnip_downstream_bias.R --args    

    - rnaseq/filter_bam.R --args  

File pipeline:

==============

Overall pipeline:

-----------------

    - RNAseq + Paresnip happen independently

    - then, paresnip_downstream_bias.R calculates downstream bias

Paresnip results:

-----------------

    - scripts/sanitise_paresnip.py

    - paresnip/paresnip_filter.R

    - paresnip/paresnip_summarise.R

    - rnaseq/paresnip_correlate_FA_SRA.R

RNAseq:

-------

    - Align to reference genome

    - If required, "samtools view -bS" to convert sam to bam

    - filter_bam.R generates target and alignment databases