SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > 454 Pyrosequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
minimum depth of coverage for transfrag extension apadr007 Bioinformatics 6 05-15-2012 06:23 AM
What is the minimum coverage needed? Annettet Illumina/Solexa 0 03-22-2011 02:41 AM
ABySS contig coverage? jgibbons1 Bioinformatics 2 09-24-2010 06:56 AM
How quantitative is contig coverage? AlexB 454 Pyrosequencing 4 09-11-2009 02:38 AM
Minimum Coverage for ChIP-Seq & RNA-Seq canis Illumina/Solexa 7 07-17-2009 01:34 AM

Reply
 
Thread Tools
Old 08-23-2012, 05:01 AM   #1
cement_head
Senior Member
 
Location: Oxford, Ohio

Join Date: Mar 2012
Posts: 232
Question Minimum contig & Coverage

Hello,

I have some 454 sequences reads from a cDNA library for a novel organism (non-sequenced genome).

I have processed the data with CLC Genomics Workbench and done four different de_novo assemblies with 200 bp, 300 bp, 400 bp and 500 bp minimal contig length. As one would expect, increasing the minimum contig length decreases the total number of contigs (or assembled cDNAs).

I have two questions:

1) Is there any consensus on the minimum contig length for cDNAs?

2) What is considered a minimal amount of coverage for any given cDNA within the final assembled contigs (cDNAs)? I would assume that rare cDNAs would have much lower coverage than abundant cDNAs.

Thanks,
CH

Last edited by cement_head; 08-23-2012 at 05:03 AM. Reason: clarity
cement_head is offline   Reply With Quote
Old 08-25-2012, 11:29 PM   #2
Torst
Senior Member
 
Location: The University of Melbourne, AUSTRALIA

Join Date: Apr 2008
Posts: 275
Default

Quote:
Originally Posted by cement_head View Post
1) Is there any consensus on the minimum contig length for cDNAs?
No. But if you throw away contigs > 500bp say, then you won't discover any transcripts that are <= 500 bp.

Quote:
2) What is considered a minimal amount of coverage for any given cDNA within the final assembled contigs (cDNAs)?
Same as for genomic DNA. That is, there is no hard rule. 1x is probably too low. 100x is probably overkill. Somewhere in between is a reasonable trade-off between getting long transcripts, and not getting false positives.

Quote:
I would assume that rare cDNAs would have much lower coverage than abundant cDNAs.
Yes. The assumption is the #reads is proportional to the #templates in the library.
Torst is offline   Reply With Quote
Old 08-26-2012, 03:27 AM   #3
cement_head
Senior Member
 
Location: Oxford, Ohio

Join Date: Mar 2012
Posts: 232
Default

Thanks - this is what I suspected.

Regards,
CH
cement_head is offline   Reply With Quote
Reply

Tags
cdna, clc genomics workbench, minimum contig length, minimum coverage

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 07:24 AM.


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