Question: How to detect segmental duplications?
0
gravatar for lamz138138
2.5 years ago by
lamz13813840
lamz13813840 wrote:

Hi!

I am interested in segmental duplications detection after de novo genome assembly. After review several papers, there are some softwares could be annotated segmental duplications, and they were rely on previously library, or need next-generation sequencing data.

It seemed only whole-genome analysis comparison pipeline (WGAC), whole-genome sequence detection (WSSD) developed by the lab of Eichler could be used (Segmental duplications: organization and impact within the current human genome project assembly and Recent segmental duplications in the human genome). However, I couldn't find relative software. Although I can try to finished the pipeline by writing scripts, some steps such as blast_end_trim may be out of my ability. So I wonder whether there are other tools for segmental duplications, or could the WGAC and WSSD available from any website?

Any suggestion would be grateful!

Best wishes!

alignment assembly genome • 1.1k views
ADD COMMENTlink modified 14 days ago by Samir140 • written 2.5 years ago by lamz13813840

My guess is that you still need to find the synteny block mapping between your case and control groups first. If you don't see a coverage difference at all in any of the synteny blocks between case and control, you might want to reevaluate your endeavour.... I could be wrong, but my understanding is that these kinds of tasks can take forever to run.

ADD REPLYlink written 6 months ago by btsui290
0
gravatar for Samir
14 days ago by
Samir140
United States
Samir140 wrote:

Look at this article and github link inside, https://academic.oup.com/bioinformatics/article/34/17/i706/5093240 Eichler lab has posted WGAC code and a detailed how-to guide at https://github.com/EichlerLab/WGAC

ADD COMMENTlink modified 11 days ago • written 14 days ago by Samir140
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1860 users visited in the last hour