hello, here are 2 lines in mm9.gold table list:
_____________________________________________________ #bin,chrom,chromStart,chromEnd,ix,type,frag,fragStart,fragEnd,strand 76,chr1,3586316,3776472,5,F,AC102110.8,23576,213732,+ 76,chr1,3776472,3868307,6,F,AC174931.2,0,91835,- ____________________________________________________ I took the second line and looked in ncbi site for this accesion: http://www.ncbi.nlm.nih.gov/nuccore/85702722 what I see is a sequence of 184558 bp, while (chromEnd-chromStart+1) equals 91835 bp at most. In addition I see that if strand is '-' then fragStart=0, and if strand is '+' then fragStart is some number >0. So what is the meaning of these columns (specifically chromStart,chromEnd,fragStart,fragEnd) and how do to determine the start and end position of mm9.gold fragments relative to the data in the NCBI site ? Many thanks, Avi _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
