--SS_lib_type FR or RF for dUTP RNA-Seq data

[Salim B]

Hi,

I have dUTP stranded RNA-Seq that I assembled as --SS_lib_type FR by mistake. When I realised my mistake, I re-assembled as  --SS_lib_type RF but decided to compare the transcript against each other.

I Megablasted one assembly against the other (-e-value 1e-20 -max-target 1). I found that the majority of transcripts match for at least one of my samples.

I suppose my question is what difference does it make to Trinity to set the --SS_lib_type to FR or RF?

Kind regards,

/SB

[Brian Haas]

Hi Salim,

The resulting assemblies should be almost identical, but one will be the reverse-complement of the other.

best,

~b

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Brian J. Haas
The Broad Institute
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[Salim Bougouffa]

Thanks. I checked the output & you are of course right

Best,

/SB