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Old 04-30-2013, 12:36 AM   #1
skm
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Default RNA-seq: how many million reads are required ?

Hi all,

I am having difficulty in assessing how many million reads are required to optimally capture a transcriptome ?.

I have typically 13 million reads from a Miseq run for 7 samples (1.85 million paired end reads/sample ). Is this number sufficient for carrying out typical RNA-seq analysis using tophat/cufflinks pipeline ? If not what is the optimal number of reads required ?

Thanks!

Regards,
SKM
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Old 04-30-2013, 01:05 AM   #2
mknut
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Depends on species. What organism are the reads from?
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Old 04-30-2013, 02:14 AM   #3
skm
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The organism is a plant (Cajanus cajan).
Any clues ?

Thanks!
SKM
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Old 04-30-2013, 03:28 AM   #4
GenoMax
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Are you only interested in the complete transcriptome or are you trying to answer a specific question (e.g. comparison of test/control)? Is there a related plant species that has been sequenced?

In general it is difficult to estimate the transcriptome size of a species. See post #2: http://seqanswers.com/forums/showthread.php?t=18018

In case of plants ploidy considerations would be another thing to keep in mind. http://gbe.oxfordjournals.org/content/2/534.full

Last edited by GenoMax; 04-30-2013 at 03:32 AM.
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Old 04-30-2013, 06:29 AM   #5
DonDolowy
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In our lab we are using RNA-seq as an alternative method to microarray. Thus, we are only interested in DEG. In our case we do 8-plexing on mouse samples on a HiSeq, which gives us approximately 20-25mio reads. This is in agreement with e.g. the guidelines for IHEC.
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