Hi Ekta, Sorry, I had misread your question and noticed that the 'specific' files you want are not in that directory.
To get this information you will have to use the table browser and (unfortunately probably have to) query one chromosome at a time to keep the file size down. - Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) - Settings: clade: Mammal genome: Human assembly: hg19 group: Genes and gene prediction tracks track: Gencode Genes table: Genecode Manual (or whichever is relevant) region: position: chr1 , ch2 , chr3, ... (one chrom per query to keep size down) output format: CDS FASTA alignment .... file type returned: gzip compressed - click "submit" - Repeat for each chromosome. Let me know if you have any additional questions: [email protected] - Greg On 3/27/11 5:31 PM, Ekta Khurana wrote: > Hi, > > I want to download CDS multiple sequence alignments for all Gencode > transcripts. > > From the download server I can download alignments for refseq and UCSC exons > but not > Gencode transcripts. > I can do this for some transcripts from the Table Browser but the dataset is > too huge to download all of it. > Could someone please let me know if there is a way to download the entire > set . > > Thanks in advance for the reply, > Ekta > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
