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Old 10-14-2010, 08:57 AM   #1
laupl
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Default is rna-seq experiment strand-specific or not?

hi all,

is there any particular field to search for understand if an rna-seq experiment is or not strand-specific on NCBI SRA db or EMBL ENA db?

thanks

laupl
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Old 10-14-2010, 12:44 PM   #2
malachig
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My impression is that a very small percentage of RNA-seq data generated to date is strand-specific. I am not aware of any way to search for this data directly in SRA. I would be very interested to hear from other users with experience querying SRA. I have found that unless you already know the accession number for the SRA data you are interested in (from a manuscript say) its very difficult to extract meaningful information from the SRA...
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Old 10-14-2010, 12:56 PM   #3
malachig
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Follow up. If you are just looking for some example data that is strand-specific... Both the iDEA Challenge and Human Body Map projects at Illumina include some directional RNA-seq libraries.
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