Tools

This page provides several tools for the analysis of Tn-Seq data, including an implementation of the non-parametric method described in Zhang et al. 2012.

jason_read_method.py [download]: Non-Parametric method (Zhang et al. 2012). This script produces output for individual sites in the genome.
- Requires python 2.7+
- Requires IGV formatted input data. See wig2igv.py converter to convert to IGV from wig formatted files.
jason_calls.py [download]: Produces calls for individual genes in the genome, using the output of non-parametric method above (jason_read_method.py).
- Requires python 2.7+
wig2igv.py [download]: Converts wig formatted files to IGV format.
- Requires python 2.7+
- Requires a GFF3 annotation file with defined coordinates, and ID or Name features.
- See http://rice.bio.indiana.edu:7082/annot/gff3.html for a description of GFF3 format.

Annotation

NC_000962.gff [download]: GFF3 annotation file for H37Rv (NC_000962) by the Broad Institute.
- Note: The ID feature of the GFF3 file utilizes sequential order to label the genes (e.g. gene0, gene1, gene2, ..., gene2085, ...).
- See the FTP site for the Broad Institute for other organisms.
H37Rv.gff3 [download]: Alternative GFF3 annotation file for H37Rv.
- Note: The ID feature of the GFF3 file utilizes the locus tag or ORF ID to label the genes (e.g. Rv0001, Rv0002, Rv0003, ..., Rv2047c, ...).

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