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
