rna-seq experiment not strand-specific or coverage symmetry

[laupl]

hi all,
i'm trying to validate a new method for the identification of sRNA in bacteria based on the analysis of RNA-seq output that seems to work on my lab data.

validation dataset was downloaded from ncbi

http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP002636

(RNA-seq on e.coli K-12 substr. W3110)

we constructed two strand specific coverage map at a single base resolution, based on alignment output procuced with SOAP.

focusing on both mRNA and ncRNA regions previously annotated, we observed a great amount of reads mapping from both coding and non-coding strand. it seems a a sort of symmetry of coverage signal.
probably I'm wrong, maybe I choose a rna-seq experiment not strand-specific? but i'm not a biologist and i'm a newbie..
someone else observe data with this behavior?
any help is greatly appreciated!

thanks

[malachig]

Yes, in all likelihood you have downloaded an RNA-seq dataset that is not strand-specific. The standard library prep in use at many centers results in sequencing of double-stranded cDNA fragments. Since the library is not stranded, you have an equal expectation of observing both strands, so the symmetry you report is not surprising. Unless the data set is specifically labeled as 'strand-specific', 'directional', etc. it is safe to assume that is not...

[qqtwee]

Yes, in all likelihood you have downloaded an RNA-seq dataset that is not strand-specific. The standard library prep in use at many centers results in sequencing of double-stranded cDNA fragments. Since the library is not stranded, you have an equal expectation of observing both strands, so the symmetry you report is not surprising. Unless the data set is specifically labeled as 'strand-specific', 'directional', etc. it is safe to assume that is not...

Hello, do you know how deal with the strand-specific RNA-seq data? which tools has the option for strand-specific information? Looking forward to your reply! Thank you! Best wishes!