Good Afternoon James: Your BLAST results are on contigs that are not in an actual assembly. They have no chromosome coordinates.
--Hiram > On 08/17/11 06:35, Zadina, James E wrote: >> The NCBI Genome blast searches produce hits in contig coordinates as >> below >> >> But and USC genome browser and the NCBI Mapviewer use chromosome >> coordinates. >> >> Is there a utility to batch convert contig to chromosome coordinates? >> >> >> >> e.g. if I condense the hits to a list of contig coordinates of the >> target/subject sequences something like the below, >> >> Can I get output in chromosome coordinates? >> >> Or can I somehow (not obvious to me) request chromosome coordinates when >> running the BLAST? >> >> >> >> 1. ref|NT_011651.17| >> <http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?maps=blast_set&db=ref_cont >> ig&na=1&gnl=ref%7CNT_011651.17%7C&gi=224514715&term=224514715%5Bgi%5D&ta >> xid=9606&RID=4EA5DVWY01P&QUERY_NUMBER=1&log$=nuclalign> >> Length=36813976..... Sbjct 33290942 XXXXXX 33290928 >> >> 2. ref|NT_011651.17| >> <http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?maps=blast_set&db=ref_cont >> ig&na=1&gnl=ref%7CNT_011651.17%7C&gi=224514715&term=224514715%5Bgi%5D&ta >> xid=9606&RID=4EA5DVWY01P&QUERY_NUMBER=1&log$=nuclalign> Length........ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
