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Old 01-16-2015, 04:36 AM   #1
anamaf_rocha
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Default RNA-Seq bacteria 2.9Mb

Hello,

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.
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Old 01-16-2015, 04:40 AM   #2
GenoMax
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Recommended coverage for RNAseq reads: https://genohub.com/next-generation-...-guide/#depth2

Claimed read output for various Ion chips: http://www.lifetechnologies.com/us/e...tem-chips.html

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.
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Old 02-05-2015, 11:53 PM   #3
chariko
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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:

http://www.ncbi.nlm.nih.gov/pubmed/23270466
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