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Tools For Visualizing Rna-Seq Splicing Graphs From De Novo Assembly Without A Reference Genome?

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!

rna-seq splicing graph assembly
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updated by guillaume.gautreau44 14 • | written by Tianyang Li 50

2 answers

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

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written by Pascal 25

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

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written by Tianyang Li 50

is this link correct ?

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written by Farbod 335

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

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written by guillaume.gautreau44 14

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