From 5723264fa6451c7b6a05e9673b67f75e3a978a40 Mon Sep 17 00:00:00 2001 From: Curtis Hendrickson Date: Fri, 4 Oct 2019 10:16:42 -0500 Subject: [PATCH] Update with description of Zhang protocol (alternate adapter2/const1-3), and conda based installation protocol --- README.md | 28 ++++++++++++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 047a2aba..78e2f438 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# TRANSIT 2.0 +# TRANSIT 2.0.2_zhang **New in Version 2.0+** @@ -13,12 +13,36 @@ - Misc. Bug fixes - **New [mailing list](https://groups.google.com/forum/#!forum/tnseq-transit/join)** - +**Verision 2.0.2_zhang changes (October, 2019)** +- change hardcoded values in tpp.py to match Zhang/Niederweis protocol + - ADAPTER2="CGACCACGACC" + - const1 = "GTCAAGTCTCGCAGATGATAAGG" + - const2 = "CTTGGTTTGGTCGTGGTCG" + - const3 = "TAACAGGTTGGCT" + Welcome! This is the distribution for the TRANSIT and TPP tools developed by the Ioerger Lab. TRANSIT is a tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. +## v2.0.2_zhang: hardcoded alternate set of adapter/const sequences. + +The easiest way to install/run this is to use Anaconda3 to create a transit enviroment, including all dependencies, +``` +conda create -n transit233 -c bioconda transit=2.3.3 bwa +``` + +Then git clone this branch of this repository +``` +git clone https://github.com/rusalkaguy/transit.git transit_v2.0.2_zhang +cd transit_v2.0.2_zhang +git checkout v2.0.2_zhang +``` + +Finally, activate the environment, but then run the cloned TRANIST/TPP (```./transit_v2.0.2_zhang/src/tpp.py ...```) + +This version should only be used for processing .fastq files into .wig files. Once you have your .wig files, please conduct statistical analyses with the latest avaiable version of TRANSIT. + ## Mailing List