is rna-seq experiment strand-specific or not?

laupl · 10-14-2010, 09:57 AM

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

malachig · 10-14-2010, 01:44 PM

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...

malachig · 10-14-2010, 01:56 PM

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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10-14-2010, 09:57 AM	#1
laupl Junior Member Location: treviso Join Date: Oct 2010 Posts: 2	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

10-14-2010, 01:44 PM	#2
malachig Senior Member Location: WashU Join Date: Aug 2010 Posts: 117	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...

10-14-2010, 01:56 PM	#3
malachig Senior Member Location: WashU Join Date: Aug 2010 Posts: 117	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.