[maker-devel] Using RNA-seq data from tophat/cufflinks in maker

[Ambrose Andongabo (RRes-Roth)]

Dear Carson,

I have been successfully running the MAKER pipeline trying to improve gene annotations. Strangely after trying to visualize my data in GBrowse  I noticed that although my density and coverage plots and even raw read plots show clearly that there is a gene feature in a particular region(confirmed by the cufflinks track), this  is not called by MAKER and thus not improving my annotation as I expected. I think the problem starts where I  converted the cufflinks gtf files to gff3 using the script you provided(cufflinks2gff3).  I will be please if you can be of any help trying to explain how I can perform the conversion so that it looks like a proper gff3 file that maker will then use to instruct the gene predictors

Many thanks in advance

Ambrose

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and we believe 
but do not warrant that this e-mail and any attachments
thereto do not contain any viruses. However, you are fully
responsible for performing any virus scanning.