Hello Deb, The number you have (13748) is correct for the current version of RefSeq. You can get this number by finding all the entries in the refGene table for which cdsStart is not equal to cdsEnd. Note that the number of items you see in the CDS fasta may be different as these entries may not map uniquely. As to why this number is different from what you see in Ensembl, the Ensembl gene set is a different set provided by a different source. If you are interested in the Ensembl gene set you can also select the following in the Table Browser to get the CDS fasta for the Ensembl gene prediction set instead:
group: Genes and Gene Prediction Tracks track: Ensembl Genes table: ensGene Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 1/5/11 11:19 AM, Deborah Ritter wrote: > Hi, > > I am tying to obtain the CDS Fasta Alignments between zebrafish and > human for all zebrafish Refseq genes. > > Is there a way to tell how many genes in zebrafish have CDS Fasta > Alignments? I want to make sure my browser did not time out and that I > have the complete file, but I can't find information on how many > zebrafish genes should be expected in this file. > > From the file I have from UCSC Table Browser, I have ~ 13,748 unique > zebrafish genes. I got this from downloading the CDS Fasta Alignments > through the DanRer6 Table Browser, grepping DanRer header lines, > extracting only the zebrafish Refseq IDs, sort -> uniq and outputting > the count of unique genes. This (13,780) is a much smaller number than > ~24,020 zebrafish genes presented by Ensembl. > > Could others please help with where I could find the expected number of > zebrafish genes for the current zebrafish build on the UCSC Genome > Browser site for zebrafish, and the expected number of zebrafish genes > with CDS Fasta Alignment to human? > > Thank you, > Deb > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
