Hi Gu, Unfortunately, we can't debug the situation from here. If the system says something is missing, see if you can't figure out why it is being claimed in the first place and from where it has gone missing. If your AXT file has scaffold_3631 in it, then it was surely in the sequence used in the alignment that made the AXT file.
If you try to find it in the sequence and it isn't there then perhaps you are using different sequences in your alignment compared to the sequence you're use later(?). Try checking your procedures to find out where scaffold_3631 is in the beginning and how it goes missing. I hope that helps! If you have any additional questions, please reply to: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 2/19/12 6:54 PM, guzhili wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
