transit

statistical calculations of essentiality of genes or genomic regions

Install

All systems
curl cmd.cat/transit.sh
Debian Debian
apt-get install tnseq-transit
Ubuntu
apt-get install tnseq-transit
image/svg+xml Kali Linux
apt-get install tnseq-transit
Windows (WSL2)
sudo apt-get update sudo apt-get install tnseq-transit
Dockerfile
dockerfile.run/transit

tnseq-transit

statistical calculations of essentiality of genes or genomic regions

This is a software that can be used to analyze Tn-Seq datasets. It includes various statistical calculations of essentiality of genes or genomic regions (including conditional essentiality between 2 conditions). These methods were developed and tested as a collaboration between the Sassetti lab (UMass) and the Ioerger lab (Texas A&M) TRANSIT is capable of analyzing TnSeq libraries constructed with Himar1 or Tn5 datasets. TRANSIT assumes you have already done pre-processing of raw sequencing files (.fastq) and extracted read counts into a .wig formatted file. The .wig file should contain the counts at all sites where an insertion could take place (including sites with no reads). For Himar1 datasets this is all TA sites in the genome. For Tn5 datasets this would be all nucleotides in the genome.