Hello. We are in the process of releasing the new gorGor3 assembly and the accompanying pairwise alignments. They should be available early next week. You may want to wait and retry your conversion with the gorGor3 files. If you are still having difficulties, please let us know.
Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of MING Chen,evolgen Sent: Tuesday, November 22, 2011 10:07 AM To: [email protected] Subject: [Genome] the supercontigs information of gorilla and the usage of axtToMaf Dear UCSC, I'm trying to convert the pairwise alignment files between human and gorilla (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsGorGor1/axtNet/ ) in axt format to maf, by using the axtToMaf program. But axtToMaf needs tSizes and qSizes. The human genome sizes is easy to get. But the gorilla genome (GorGor1)size is difficult to find, especially for supercontigs. I have searched NCBI WGS ( http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CABD01 ) and Ensembl (ftp://ftp.ensembl.org/pub/release-57/fasta/gorilla_gorilla/dna/ ). But there is no supercontig information matching your pairwise alignment files, for example: 0 chr1 10974 20818 Supercontig_0000035 107816 117704 + 890977 So could you please tell me where I can find the correct information about the supercontigs, especially their length information ? Could you please explain about the function of tSizes and qSizes in the axtToMaf program? Is it necessary for them to be accuracy? Thanks very much Plus: the pairwise alignment assembles: target/reference: Human (hg19, Feb. 2009, GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1)) query: Gorilla (gorGor1, Oct. 2008, Sanger Institute Oct 2008 (NCBI project 31265, CABD01000000) Chen Ming Evolutionary Genomics (Evolgen) CAS-MPG Partner Institute for Computational Biology (PICB) Shanghai Institutes for Biological Sciences(SIBS) Chinese Academy of Sciences (CAS) 320 Yue Yang Rd. Shanghai, P.R.China 200031 TEL: +86-21-5492-0467 http://www.picb.ac.cn/evolgen/ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
