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Old 03-21-2013, 09:42 AM   #1
trombidu
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Default Question on directional and non-directional RNA-seq

Hi,

I would like to get some RNA-seq data from NCBI to test our method, but I am not sure the given data are strand-specific or not. How can we know that, please?

Thank you very much.
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Old 03-24-2013, 05:00 PM   #2
Dario1984
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It is not very rigorous, but you can download the mapped data, load it into a genome browser, then look at some highly expressed known genes. Do you see many reads in both directions, or almost all reads in one direction ?
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Old 03-24-2013, 10:17 PM   #3
dietmar13
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Default RSeQC

RSeQC checks for strand specificity...

http://code.google.com/p/rseqc/
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Old 03-25-2013, 02:39 AM   #4
trombidu
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Thanks a lot.
Mapped data are not always available. So we look for kind of keywords which imply strand specificity.
A tool like RSeQC does help.
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