Dear sir, Thank you very much for your help in the last mail that you told us the place to download the 2bit genome files. Using these genomes, we successfully generated syntenic Axt files and converted them to maf files. But we still met a problem in the work of the aplaca genome.
After we generated the syntenic Axt files in aplaca, we met a problem during the process of converting the synAxt files to maf files. The error message is "'scaffold_3631' not found". All of the files are downloaded at your site. The 2bit genome file is from ftp://hgdownload.cse.ucsc.edu/gbdb/vicPac1/vicPac1.2bit. chain and net files are from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsVicPac1/. The sizes file used for converting maf files is from genome.cse.ucsc.edu/cgi-bin/hgTables?submit=submit&hgta_doTopSubmit=1&hgta_table=chromInfo&hgta_outputType=primaryTable&hgta_regionType=genome&hgta_track=gold&db=vicPac1. Is that due to the mismatch of the sizes file? We are looking forward to your reply. Best, Gu Zhili 2012-02-19 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
