Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
mouse miRNA seq with SOLiD, help with coverage needed desperately! bisrat SOLiD 2 06-29-2010 03:37 AM
Where can I find the complete FASTA format sequence(human and mouse)? iloveneworleans Bioinformatics 5 02-24-2010 05:00 PM
PubMed: Transcriptome-wide identification of novel imprinted genes in neonatal mouse Newsbot! Literature Watch 0 12-05-2008 06:02 AM
In Sequence: Researchers Use SOLiD to Study Gene Expression in Single Mouse ES Cells Newsbot! SOLiD 0 11-04-2008 02:00 PM
In Sequence: Yale Team Uses an Illumina GA to Sequence Yeast Transcriptome; Finds Gre Newsbot! Illumina/Solexa 0 05-06-2008 03:02 PM

Thread Tools
Old 06-29-2010, 07:33 AM   #1
Junior Member
Location: south america

Join Date: Jun 2010
Posts: 2
Default how much sequence is needed to cover a mouse transcriptome

Hi all, I am looking for a way to estimate the sequencing space needed to get a reasonable coverage of a transcriptome. Initially I am interested in rat and mouse, but if there is a rule of thumb or a place where I can check for this type of calculations.
thanks a lot for any thoughts or advice


jrss is offline   Reply With Quote
Old 06-29-2010, 07:46 AM   #2
Senior Member
Location: Boston area

Join Date: Nov 2007
Posts: 747

75M tags is what some vendors shoot for on a mammalian transcriptome (for example, on SOLiD4 this works out to 10 samples / slide). I've been meaning to look at the recent papers to try to work it out, though it can be a slog finding the numbers on a library-by-library basis.
krobison is offline   Reply With Quote
Old 08-23-2010, 08:33 PM   #3
Senior Member
Location: WashU

Join Date: Aug 2010
Posts: 117

In my experience it depends a lot on what you consider 'reasonable' coverage. If you only want to profile gene level expression you don't need much. If you want to have a fair chance of detecting every isoform of every gene, you need at least an order of magnitude more reads. I have analyzed ~100 mouse and human transcriptomes using 'ALEXA-Seq'. When asked this question and forced to give a specific number I usually say that ~100 million paired reads is a good target. In practice it depends on many factors such as the mappability of your reads (which is highly dependent on the error rate at your center). I have also encountered some tissues that had extremely high expression of a small number of genes, and this consumed a lot of read depth. Other tissues did not suffer from this affect as much. You can see the outcome of analyzing some example mouse tissues sequenced to a depth of ~100 to ~250 million paired reads here:
malachig 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 11:27 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO