Hello Chen Ming, I would like to add a bit about these parts of your question:
> So could you please tell me where I can find the correct information > about the supercontigs, especially their length information ? We have a shell script fetchChromSizes that retrieves the sizes. You can download the script here: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes Run "fetchChromSizes" with no arguments to see usage instructions. > Could you please explain about the function of tSizes and qSizes in > the axtToMaf program? Is it necessary for them to be accuracy? MAF's "s" and "e" blocks have a srcSize field (see http://genome.ucsc.edu/FAQ/FAQformat.html#format5). AXT does not include that info, so axtToMaf takes it from the tSizes and qSizes input files. MAF's inclusion of chromosome sizes makes it possible to calculate forward-strand coordinates from the reverse-strand coordinates when the strand field is "-". Hope that helps, Angie ----- Original Message ----- > From: "MING Chen,evolgen" <[email protected]> > To: [email protected] > Sent: Tuesday, November 22, 2011 10:07:27 AM > 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
