Virtual Machine for Hyper-TRIBE Analysis
Description
To facilitate analysis of RNA sequencing data generated from mammalian HyperTRIBE experiments we have generated the following virtual machine with the following software installed:
bedtools suite (v2.16.2, 2.26.0 or later): http://bedtools.readthedocs.io/
Bowtie2 (v2.1.0, v2.2.9): http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Cutadapt: https://cutadapt.readthedocs.io/en/stable/installation.html
HyperTRIBE software: https://github.com/rosbashlab/HyperTRIBE
MariDB v10.1 or later https://downloads.mariadb.org/
Perl (v5.8.8, v5.12.5, v5.22.1): https://www.perl.org/get.html
Perl Module: DBI.pm (v1.631, v1.636)
Perl Module: DBD:mysql (v4.042)
Picard (v2.8.2): https://broadinstitute.github.io/picard/
Python (v2.7.2 or later): https://www.python.org/downloads/
SAMtools (v1.3.1): http://samtools.sourceforge.net/
SRA Toolkit (v2.10.8): https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
STAR (v2.7.3a): https://github.com/alexdobin/STAR
Stringtie: https://ccb.jhu.edu/software/stringtie/
Trimmomatics (v0.36): http://www.usadellab.org/cms/?page=trimmomatic
Files
Files
(5.9 GB)
Additional details
Related works
- Is derived from
- Journal article: 10.1016/j.isci.2020.101318 (DOI)
References
- Biswas, Jeetayu et. al. (2020), iScience . 2020 Jul 24;23(7):101318. doi: 10.1016/j.isci.2020.101318. Epub 2020 Jun 28.