Strand information in GTF

[samha...@gmail.com]

Hi Yashar,

We are currently trying to use the gtf file for a differential expression analysis project. However, I notice that a small but significant number of features do not contain any strand information, (i.e. column 7 should be + or -, but some are .).

As such, we are having trouble aligning our reads with TopHat2 as it requires a gtf with strand information.

Do you have a version which has the complete strand information for all lncRNAs, please?

Look forward to your reply and best wishes,

Sam

[Yashar Niknafs]

Hello,

An unstranded transcript means it was built from underlying RNA-seq data with no strand information, so there is no way to impute strand from that. 

It is a tricky thing. It could be a real monoexonic previously unidentified gene. But there it may be hard to investigate such transcription. If we had more strand-specific data, we could get more clarity on these types of transcripts, but with what we have at our disposal now, its a bit tough. 

-Yashar 

[samha...@gmail.com]

Hi Yashar,

Thank you very much for your quick response and for your explanation. I think for now we will either omit these targets or perhaps treat them as 'unstranded' and accept hits on either strand.

Thanks again and best wishes,

Sam