SeqMonk
What is SeqMonk? SeqMonk [1] is a program for visualising and analysing large set of mapped genomic regions. It was desgined to work with data from high throughput sequencing technologies, but will work just as well with any set of mapped reads (link). SeqMonk provides a genome browser which allows you to navigate quickly around an annotated genome and a data browser which puts your sequence reads in their appropriate genomic context. It also includes a set of tools to allow you to quantitate and filter your data so that you can find regions of interest in a systematic way.
What is SeqMonk useful for? SeqMonk was designed to be as flexible as possible and should be useful in a wide variety of experimental designs. Types of experiment which are known to have been successfully analysed with SeqMonk are:
- ChIP-Seq
- Chromosome Conformation Capture
- High-throughput Bisulphite Sequencing
- Analysis of genomic deletions/duplications
The software as well as tutorial material is installed on the BioWare machine.
More information can be accessed on the website (course and advanced course).
Video tutorials
rem: click on the playlist icon to switch to other videos
References:
- ↑
Tarjei S Mikkelsen, Manching Ku, David B Jaffe, Biju Issac, Erez Lieberman, Georgia Giannoukos, Pablo Alvarez, William Brockman, Tae-Kyung Kim, Richard P Koche, William Lee, Eric Mendenhall, Aisling O'Donovan, Aviva Presser, Carsten Russ, Xiaohui Xie, Alexander Meissner, Marius Wernig, Rudolf Jaenisch, Chad Nusbaum, Eric S Lander, Bradley E Bernstein
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.
Nature: 2007, 448(7153);553-60
[PubMed:17603471] ##WORLDCAT## [DOI] (I p)
