Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent

Similar Threads
Thread Thread Starter Forum Replies Last Post
how to caculate rpkm for bacteria RNA-SEQ data? joyjane88 RNA Sequencing 4 10-18-2013 02:32 AM
Bacteria intergenic regions RNA-seq honey Bioinformatics 1 04-18-2013 07:07 AM
Optimal coverage for RNA-seq analysis of DGE in bacteria seb330 RNA Sequencing 3 11-14-2012 05:42 PM

Thread Tools
Old 01-16-2015, 04:36 AM   #1
Junior Member
Location: Portugal

Join Date: Jun 2013
Posts: 2
Default RNA-Seq bacteria 2.9Mb


What is the recommended number of reads for RNA-Seq (whole transcriptome) of bacteria with genome size of 2.9Mb? I saw about 10 million reads for differential expression. How do I calculate how many samples I can put in a Ion PGM/Proton chip with this information? And human?

Thanks in advance.
anamaf_rocha is offline   Reply With Quote
Old 01-16-2015, 04:40 AM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,978

Recommended coverage for RNAseq reads:

Claimed read output for various Ion chips:

You can combine this information to calculate an "ideal" number. In practice you will want to allow for 15-25% less yield just to be safe.
GenoMax is offline   Reply With Quote
Old 02-05-2015, 11:53 PM   #3
Location: Spain

Join Date: Jun 2010
Posts: 56

The fact is if you want to detect rare variants or just doing a normal differential expression analylisis. Also if you include biological replicates (highly recommended 3 replicates per condition)for your experiment, you could also reduce the coverage.

A recent paper (detailded below) indicated that above 13 million would relatively little increase the number of genes detected. They said that 2-3 million fragments per sample enabled a significant number of genes differentially expressed by 2 fold or more.

I would recommend to have a look at:
chariko is offline   Reply With Quote

rna-seq advice, rna-seq bacterial, transcriptomes

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 06:02 PM.

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