Refflat file for Rattus norvegicus

Question

[AIMAR]

Hi everyone, hope everyone is doing well

Is there anyone here who can help me to obtain the refFlat file for the Rat (Rattus norvegicus). I'm actually working on RNA-seq project that requires that file.

I'm using the last genome, transcriptome and GTF file from NCBI database. So if you any tool that could help me to generate the refFlat or database that I can download it, it will be very helpful.

Thanks in advance !

Answer 1

[GenoMax]

Links below are for the latest Rat assembly available at UCSC. Change the assembly, if you need something older.

You can export the data from UCSC Table browser in RefFlat format using this link: https://genome.ucsc.edu/cgi-bin/hgTables?clade=mammal&org=Rat&db=rn7&hgta_group=allTables&hgta_track=rn7&hgta_table=refFlat

If you need the format then you may as well get the matching genome and GTF files from UCSC: https://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/

If you want to stick with NCBI then you can covert the GTF file to RefFlat using: https://palmerlab.org/converting-gff3-to-refflat/

[AIMAR]

Thanks very much for all. I guess I'll change genome version ;)