Hi Weiwei,
Thank you for your question about a isSizeLink error while building a
bigBed file. The problem is that the fields of your autoSql file do
not match the official bed12 standards. The first 12 fields of your
goat.as file should instead be:
table bed
"Browser extensible data"
(
string chrom; "Reference sequence chromosome or scaffold"
uint chromStart; "Start position in chromosome"
uint chromEnd; "End position in chromosome"
string name; "Name of item"
uint score; "Score from 0-1000"
char[1] strand; "+ or -"
uint thickStart; "Start of where display should be thick (start codon)"
uint thickEnd; "End of where display should be thick (stop codon)"
uint reserved; "Used as itemRgb as of 2004-11-22"
int blockCount; "Number of blocks"
int[blockCount] blockSizes; "Comma separated list of block sizes"
int[blockCount] chromStarts; "Start positions relative to chromStart"
)
You could also declare your bigBed as type=9+4 to avoid changing your .as file:
bedToBigBed -as=
goat.as -type=bed9+4 goat.bed.new.sorted
../chrom/chrom.sizes
goat.bb
Please let us know if you have any further questions!
Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to
gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to
genom...@soe.ucsc.edu.
Christopher Lee
UCSC Genomics Institute
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