upstream open reading frame gene filteration

Question

[ashkan]

Hi Guys,

I have RNA-seq data and want to filter the genes with "upstream open reading frame". do you guys know how to do that? thanks

[Farbod]

Hi,

Have a look at this please:

http://upep-scmb.biosci.uq.edu.au/

or you can assemble your reads and then use : http://transdecoder.github.io/

[glihm]

Hi,

Can you give us more details please ?

Do you want to extract genes with upstream open reading frames (uORF) from Fastq files (reads from sequencing) ? From your annotation file (GFF) ?

[ashkan]

so far I have only fastq files. indeed I want to get rid of those genes with upstream open reading frames (uORF) and filter them from my raw data file.