SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
Velvet Assembler: expected coverage versus estimated coverage versus effective covera DMCH Bioinformatics 1 11-30-2011 04:21 AM
"nucleotide coverage" to genome feature coverage sheremey Bioinformatics 3 11-02-2010 11:24 AM
low 454 coverage combined with high solexa coverage strob Bioinformatics 7 10-07-2010 10:14 AM
coverage neoanderson 454 Pyrosequencing 3 04-05-2010 05:16 AM
Coverage suludana Illumina/Solexa 1 12-15-2008 10:51 AM

Reply
 
Thread Tools
Old 02-21-2012, 05:37 AM   #1
swaraj
Member
 
Location: Naples, Italy

Join Date: Feb 2012
Posts: 50
Default Coverage

Dear All,
I am curious to know for a RNAseq experiment what would be the ideal statistics to measure the coverage of reads across known features. The options I am confused with are whether I should go with coverage of complete transcripts or simply work on the coverage of exons. Also there are some transcripts which have high coverage on only one of the exons hence how to interpret such results.
swaraj is offline   Reply With Quote
Old 02-21-2012, 05:40 AM   #2
swaraj
Member
 
Location: Naples, Italy

Join Date: Feb 2012
Posts: 50
Default

Also I would like to know whether I can use a coverage cut-off to select for the expression of a transcript.
swaraj is offline   Reply With Quote
Old 02-21-2012, 05:56 AM   #3
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

Transcripts. FPKM, not coverage. Even if you are not using the program, see the cufflinks manual for a good explanation and a reference. http://cufflinks.cbcb.umd.edu/howitworks.html
westerman is offline   Reply With Quote
Old 02-21-2012, 07:01 AM   #4
swaraj
Member
 
Location: Naples, Italy

Join Date: Feb 2012
Posts: 50
Default

I am working with non-coding transcripts for whom the FPKM as reported by cufflinks is very low. Many times the FPKM value reported is zero whilst I see coverage of the built transcripts. This behaviour may be because some classes of non-coding transcripts are be expressed in a small spatio-temporal window. Hence my question, that whether I can use some score like coverage or read count instead of FPKM to monitor such transcripts. My apologies for not elaborating on the context of the question before.
swaraj is offline   Reply With Quote
Old 02-21-2012, 07:33 AM   #5
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

Quote:
Originally Posted by swaraj View Post
I am working with non-coding transcripts for whom the FPKM as reported by cufflinks is very low. Many times the FPKM value reported is zero whilst I see coverage of the built transcripts. This behaviour may be because some classes of non-coding transcripts are be expressed in a small spatio-temporal window. Hence my question, that whether I can use some score like coverage or read count instead of FPKM to monitor such transcripts. My apologies for not elaborating on the context of the question before.
I guess I am at a loss as to what you are asking. Certainly you can use read counts. I have done so many times. Statistically you will probably run into problems proving anything from them (especially if they are low) unless you are working in a binary on-off situation.

Assuming that you are not in a binary situation then with zero FPKMs and low counts then you are in the "noise level". Using the counts as a way to point towards other experiments is acceptable. Using the counts in a paper would be tricky since I would expect the reviewers to question any conclusion made from noisy data.
westerman is offline   Reply With Quote
Old 02-21-2012, 07:55 AM   #6
swaraj
Member
 
Location: Naples, Italy

Join Date: Feb 2012
Posts: 50
Default

Thanks a lot for your valuable suggestions. I will keep them in mind.
swaraj is offline   Reply With Quote
Reply

Tags
coverage, exon, rnaseq, transcript

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 01:16 PM.


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