How to obtain a refFlat file for the Rat

Question

[AIMAR]

Hi everyone, I would like to obtain the refFlat.txt file for the rat, but I didn't find anywhere.

If there's anyone here who can help me it'll be helpful cause I'm on a project that requires the refFlat file.

Thanks !

Answer 1

[GenoMax]

Please don't ask the same question again in a new thread. This was answered a few weeks back: Refflat file for Rattus norvegicus

Change the genome version on the page I linked in answer above if you need something other than rn7 build.

[AIMAR]

I've try the mentioned methods but nothing work that's why I've asked again If I can find a new solution.

Thanks !

[GenoMax]

but nothing work

What does not work? Once you export a file from the link included, it is in refFlat format.

[AIMAR]

I've download file from the UCSC Table browser tool, but when I used it with gatk collectRnaseqMetrics, there's gene that are not recognize.

[GenoMax]

You can't mix and match genomes and annotation as we discussed in the prior thread. Are you using the genome from UCSC, if you are using the RefFlat file from there.