Table 1.
Summary of computational tools used to analyze RNA-Seq and ChIP-Seq data.
| Software | Purpose | Location | URL |
|---|---|---|---|
| TopHat/Bowtie | RNA-Seq: alignment of spliced reads to the reference genome (NC_002505.1 and NC_002506.1). | Galaxy Tool Shed | https://galaxy.uabgrid.uab.edu |
| Cufflinks | RNA-Seq: generation of differential gene expression reports. | Galaxy Tool Shed | https://galaxy.uabgrid.uab.edu |
| CASAVA v1.8.2 | ChIP-Seq: conversion of .bcl files into .fastq.gz files. | Illumina web site | http://support.illumina.com/sequencing/sequencing_software/casava.html |
| Bowtie | ChIP-Seq: alignment of short reads to the reference genome to generate .SAM files. | Galaxy Tool Shed | https://galaxy.uabgrid.uab.edu |
| SAM tools | ChIP-Seq: filtering and removal of unmapped reads and conversion of .SAM to .bam files. | Galaxy Tool Shed | https://galaxy.uabgrid.uab.edu |
| SeqMonk v0.27.0 | ChIP-Seq: peak calling using the MACS algorithm [9]; quantitation using the Read Count Quantitation algorithm and annotation of H-NS binding sites. | Babraham Institute | http://www.bioinformatics.babraham.ac.uk/projects/seqmonk |