vanopijnenlab / magenta

MAGenTA: Microbial Assessment by Genome-wide Tn-Seq Analysis

A suite of tools for Tn-Seq data analysis

What is Tn-Seq?

This repository contains tools and documentation for Transposon-Sequencing (Tn-Seq) data analysis. Tn-Seq combines transposon insertional mutagenesis with high-throughput sequencing of the transposon insertion sites to identify genes contributing to a function of interest in bacteria. For more information on Tn-Seq as a method, several scientific papers have been published with detailed explanations:

• Van Opijnen, T., Bodi, K. L., & Camilli, A. (2009). Tn-seq; high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nature Methods, 6(10), 767–772. http://doi.org/10.1038/nmeth.1377 Pubmed
• Van Opijnen, T., & Camilli, A. (2013). Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms. Nature Reviews. Microbiology, 11(7), 10.1038/nrmicro3033. http://doi.org/10.1038/nrmicro3033 Pubmed
• Van Opijnen, T., & Camilli, A. (2012). A fine scale phenotype–genotype virulence map of a bacterial pathogen. Genome Research, 22(12), 2541–2551. http://doi.org/10.1101/gr.137430.112 Pubmed
• Van Opijnen, T., Dedrick, S., & Bento, J. (2016). Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome. PLoS Pathogens, 12(9), e1005869. http://doi.org/10.1371/journal.ppat.1005869 Pubmed

MAGenTA Manual

See documentation/magentaManual.pdf for the full manual. This manual will help you to process data from either of these methods and with a little imagination probably any other variation you may use.

MAGenTA Tools

See tools/ for command-line and galaxy tools as well as workflows for galaxy. As described in the full manual, all tools are implemented in the galaxy public tool shed and available for download there.

magenta's Issues

WARNING:galaxy.model:Datatype class not found for extension 'map'

When running the enhanced bowtie mapper, I get the error:

WARNING:galaxy.model:Datatype class not found for extension 'map'

Do I need to add this datatype to Galaxy somehow? I'm assuming the calculate fitness script requires this format, and SAM formatted data will not work. Is that correct?

Commandline Issue

Hi
I am attempting to test this software with our TnSeq test Dataset and got the following error in the calc_fitness step:

Starting: 11:16:56.980784
Done generating feature lookup: 11:16:57.771881
Read first file: 11:18:03.000280
Read second file: 11:18:41.338094
Reads:
1: + 5048023 - 4872901
2: + 4364013 - 4566853
Sites:
1: + 5048023 - 4872901
2: + 4364013 - 4566853
Cfactor 1: 1.0525179837
Cfactor 2: 0.947482016297
Done comparing mapfiles 11:19:07.034614
Genic: 0
Total: 617054

Traceback (most recent call last):
File "/local/projects-t2/achatterjee/magenta/tools/commandline/calc_fitness.py", line 382, in
with open(arguments.outfile2, "w") as f:
TypeError: coercing to Unicode: need string or buffer, NoneType found

Here is my command:

/usr/local/packages/python-2.7.14/bin/python calc_fitness.py -ref sequence.gb.txt -t1 R1_trimmed.fastq.strict.map -t2 R2_trimmed.fastq.strict.map -out calc_fitness_out_strict.csv -cutoff2 0 -b BOTTLEALL -uncol UNCOL

I appreciate your help!
Apaala

No link to the Galaxy toolshed in docs?

is it just tools?
is it just a workflow?
or is it both?
are there any docs?

Tool id in Randomly Sheared Data Prep.ga for bowtie wrapper is incorrect

The tool id for bowtie in the Randomly Sheared Data Prep.ga is enhanced_bowtie_wrapper, however, the tool in the toolshed is enhanced_bowtie_mapper (mapper vs. wrapper). An actually, the tool id is bowtie_mapper