SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
De novo transcriptome quality metrics? LizBent De novo discovery 7 06-25-2015 03:56 AM
Mapping paired reads to de novo RNA-seq assemblies for quality assessment? BobFreemanMA Bioinformatics 1 08-02-2012 11:36 AM
FASTQC for checking quality of 120 bp reads madsaan Bioinformatics 4 06-06-2011 11:17 PM
TopHat Checking for Bowtie [Failed] ercfrtz Bioinformatics 1 03-14-2011 01:43 PM
PubMed: High-quality draft assemblies of mammalian genomes from massively parallel se Newsbot! Literature Watch 1 01-31-2011 06:57 AM

Reply
 
Thread Tools
Old 02-20-2010, 12:16 AM   #1
ShellfishGene
Member
 
Location: Germany

Join Date: Mar 2009
Posts: 14
Default Quality checking transcriptome assemblies

Dear all,

I am currently working on 454 transcriptome data. I have assembled the reads using the current newbler version, MIRA, and will try Velvet/Oases later on.
However, I am still not sure how to decide on one assembly to use for all further analysis. Comparing the basic statistics like contig length, reads per contig, N50 and so on only gives hints to which may be the better assembly. From these stats I would have choosen the newbler assembly, but they do not really tell me how well the transcripts are assembled. Alternative splicing and gene copies can make for bad assemblies, for example.
Some methods I thought of that may tell me more are looking at single genes that have a known sequence, and check how the transcripts for these genes are assembled. However, that has to be done manually, and is only possible for a few genes.
Maybe one could also blast all contigs and check which assembly gives more or better hits, or how many hits one contig has on average. Too many hits per contig could maybe mean that multiple transcripts are assembled to one contig.

How do you check assembly quality beyond the basic stats? Without a sequenced genome, of course.

Cheers,

Till
ShellfishGene is offline   Reply With Quote
Old 02-20-2010, 06:44 AM   #2
Xi Wang
Senior Member
 
Location: MDC, Berlin, Germany

Join Date: Oct 2009
Posts: 317
Default

It is mentioned by Oases that the transcriptome assembly is quite different from genome assembly, due to the alternative splicing and different gene expression levels. Therefore, the old statistics may not be applicable to transcriptome assembly.
__________________
Xi Wang
Xi Wang is offline   Reply With Quote
Reply

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 09:13 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO