Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
DeNovo assembly using pacBio data krittika.sasmal Pacific Biosciences 50 06-05-2013 09:56 AM
Denovo assembly problem huma Asif Illumina/Solexa 1 03-27-2013 09:20 PM
TGICL for denovo transcriptome gfmgfm Bioinformatics 16 01-24-2013 03:59 PM
SOAP denovo assembly results bioinfosm Bioinformatics 9 06-13-2012 07:22 AM
GO classification on denovo transcriptome Temima RNA Sequencing 0 03-09-2011 02:28 AM

Thread Tools
Old 10-28-2009, 01:42 AM   #1
Uwe Appelt
Location: Heidelberg, Germany

Join Date: Oct 2009
Posts: 27
Default DeNovo Transcriptome Assembly (human)

Dear all,

i currently need to compare two transcriptomes - lets say, one untreated the other treated. Each of both cDNA-samples has been 36bp-paired-end-sequenced on two lanes (Illumina), such that i have 10e6 untreated and about 15e6 treated paired reads.
Primarily i want to discover structural changes in the treated transcriptome with respect to the untreated one. This includes genetic recombinations, splice variants and large transcriptional inserts similar to transposons.
My question is, how i could establish such an analysis. The recombination/inserts things make non-de-novo (hence comparative) assemblers appear inappropriate. Now, my initial idea is, to use Velvet/Abyss to build the two assemblies de novo, to align them in a second step against each other. Does this make sense to you guys? Or is there even a package out there, which i don't know yet?

Thanks in advance for any comments on that!

Uwe Appelt is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 06:03 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO