Good Afternoon Neel: We do not separate the coding from non-coding genes in our Ensembl gene track on Danio Rerio.
You can fetch the GTF file directly from Ensembl and filter it for non-coding genes, for danRer6: wget -O /dev/stdout \ "ftp://ftp.ensembl.org/pub/release-59/gtf/danio_rerio/Danio_rerio.Zv8.59.gtf.gz"; \ | zcat | grep -v protein_coding \ | sed -e "s/^\([0-9XY][0-9]*\)/chr\1/; s/^MT/chrM/" The 'grep -v protein_coding" eliminates protein coding genes. The sed command changes Ensembl chromosome names to UCSC names. Our danRer7 browser is under construction, soon to be released in the new year. The Ensembl genes for that version are: wget -O /dev/stdout \ ftp://ftp.ensembl.org/pub/release-60/gtf/danio_rerio/Danio_rerio.Zv9.60.gtf.gz \ | zcat | grep -v protein_coding \ | sed -e "s/^\([0-9XY][0-9]*\)/chr\1/; s/^MT/chrM/" --Hiram ----- Original Message ----- From: "Neel Aluru" <[email protected]> To: [email protected] Sent: Tuesday, December 28, 2010 12:04:21 PM Subject: [Genome] Danio Rerio annotation GFF file Hello, I have read in a very old post in the mailing list archive that non coding ensembl genes will be available in the genome browser. I cannot find it in the website. I may be looking at the wrong place. If it is available, could you please guide me how to get it. Thank you, Neel Neel Aluru Postdoctoral Scholar Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543 USA 508-289-3607 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
