Please note, the measurement you describe is a simple measure of how much of the genome has been used to calculate phastCons measurements. You have not calculated the conserved elements of the 46 genomes. Please note the description of the numerous tables related to this large composite track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way
You may be interested in the "most conserved" elements table, for example the "vertebrate" most conserved elements: http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=compGeno&hgta_track=cons46way&hgta_table=phastConsElements46way&hgta_doSchema=describe+table+schema The table browser measures this track to indicate: item count 5,163,775 item bases 146,751,970 (5.07%) item total 146,751,970 (5.07%) smallest item 1 average item 28 biggest item 17,443 smallest score 177 average score 338 biggest score 1,000 --Hiram ºú½ wrote: > Hi, > I am interested in phastCons conserved elements for multiple alignments of > 45 vertebrate genomes to the human genome ; > so I have downloaded bed file by using the Table Browser: > http://genome.ucsc.edu/cgi-bin/hgTables. With the following selections: > clade: Mammal > genome: Human > assembly: Feb. 2009 (GRCh37/hg19) > group: Comparative Genomics > track: Conservation > table: Vertebrate Cons (phastCons46way) > region: genome > filter/Limit data output to: 10,000,000 > output format: bed format > > After downloaded this bed file,I measured the coverage of all.bed with a > command such as: > grep '^chr' all.bed | awk '{total += $3 - $2} END {print > total/3,137,146,256 }' > where 3,137,146,256 is the total number of bases of the human genomic > sequence, > all.bed is the name what I have downloaded . > > The result is 0.9069;so I have a question about this : > Why it is so large ? or why are so many conserved elements for multiple > alignments of 45 vertebrate genomes to the human genome ? > > So is there any problem about the bed file ? > or can you tell me the parameters when running the program PhastCons and how > do you estimate the parameters ? > > > Thkan you! > Really appreciate your help! > Best wishes for you! > > 2011-12-27 > > > Jiang Hu _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
