Question: Tools For Visualizing Rna-Seq Splicing Graphs From De Novo Assembly Without A Reference Genome?
1
gravatar for Tianyang Li
6.7 years ago by
Tianyang Li490
Beijing, China
Tianyang Li490 wrote:

Hi

Are there existing tools for visualizing RNA-Seq splicing graphs from de novo assembly without a reference genome?

What I'd like is something that can show how read goes from one exon to another and the coverage of each exon.

Are there such tools using only contigs assembled by a de novo assembler and the reads?

Thanks!

assembly splicing rna-seq graph • 4.2k views
ADD COMMENTlink modified 3.3 years ago by guillaume.gautreau44140 • written 6.7 years ago by Tianyang Li490
3
gravatar for Pascal
6.7 years ago by
Pascal250
European Union
Pascal250 wrote:

Hi,

take a look at "CBrowse". It is made for de novo assemblies and works with SAM/BAM files. I haven't used it myself, but I think this is what you want.

Here is the link to the publication: http://bioinformatics.oxfordjournals.org/content/early/2012/07/12/bioinformatics.bts443.abstract

And their web site: http://www.conifergdb.org/CBrowse

ADD COMMENTlink written 6.7 years ago by Pascal250
1

is this link correct ?

ADD REPLYlink written 2.8 years ago by Farbod3.2k

This appears to be the new home of CBrowse.

ADD REPLYlink written 2.8 years ago by genomax65k

I've looked at this paper but it seems it's too complicated to set up and its functionality is a bit lacking.

ADD REPLYlink written 6.7 years ago by Tianyang Li490
1
gravatar for guillaume.gautreau44
3.3 years ago by
France
guillaume.gautreau44140 wrote:

I suggest : Bandage https://rrwick.github.io/Bandage/

ADD COMMENTlink written 3.3 years ago by guillaume.gautreau44140
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: 758 users visited in the last hour