IMPORTANT NOTICE

gwide is obsolete. Most of its functionalities have been replaced by trxtools(https://github.com/TurowskiLab/trxtools).

OBSOLETE PACKAGE gwide

Python package for downstream analysis of CRAC data. Package developed for analysis of RNA polymerase III data published in Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts. Turowski TW, Leśniewska E, Delan-Forino C, Sayou C, Boguta M, Tollervey D. Genome Res. 2016 May 20. pii: gr.205492.116. http://www.ncbi.nlm.nih.gov/pubmed/27206856

Installation

for users:

pip install --user mercurial git+git://github.com/tturowski/gwide.git (or skip --user mercurial to install globally);

add to your .profile or .bash_profile or .bash_login:

PATH="$HOME/.local/bin:$PATH"

for developers:

git clone git@github.com:tturowski/gwide.git pip install --editable .

Setup

It's possible to create $HOME/bin/default.aml file with paths to follwing files: #default paths to genome files GTF_PATH : *.gtf FASTA_PATH : *.fasta TAB_PATH : *.tab

Description

ploting of genome-wide plots pyCRAC downstream tool

gwideHittable (-h for help, input *.hittable) - Three options:

• Calculate "correlations": Pearson, Spearman or Kendall Tau
• "count" hittables for further analysis. Ideal to work with multiple experiments
• Plot "piechart"s for hittable classes (plots are not ideal...)

novo2concat.py (-h for help):

• copy *.novo files to new folder
• prefix from *.novo file is used as experiment name

gwidePlot (-h for help, input *.concat):

• plot genome wide plots, 5' and 3' end aligned or aligned to choosen aligner (-o aligner) or aligneg to 3' end of read-through
• plot genome wide ratio between different experiment
• possibility to filter genes using -f option
• printing *.csv tables to generate heatmaps using other software (i.e. GENE-E)
• calculate p-value for a non-canonical termination sites
• making GTF files (for whole transcripts or only for extensions

gwidetRNA (-h for help, input *.concat):

• plot single tRNA plots: multiple experiments per page, one experiment per page, one experiment under another, mark A and B boxes
• plot ratio between experiments
• plot under nucleotides resolution
• calculate dG RNA_DNA/DNA_DNA for each valley or last 20 nt after tRNA gene
• save tab-deliminated file with each plot calculations

GTF parser tools (-h for help, work with standard input):

• getFastaSeqs
• getGeneLength
• getIdFromName
• getNameFromId
• getGeneNamesFromGTF
• getNameFromId4Tab

Citation

Turowski TW, Leśniewska E, Delan-Forino C, Sayou C, Boguta M, Tollervey D. Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts. Genome Res. 2016 May 20. pii: gr.205492.116.

Note

This project has been set up using PyScaffold 2.4.4. For details and usage information on PyScaffold see http://pyscaffold.readthedocs.org/.