isSizeLink error when use bedToBigBed program

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Fu weiwei

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Jun 21, 2017, 11:38:44 AM6/21/17
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Dear UCSC Genome Browser Team,
 
I am trying to convert bed file to bigBed format. However, the bedToBigBed command returned one error, the details is as follows:
bedToBigBed -as=goat.as -type=bed12+1 goat.bed.new.sorted ../chrom/chrom.sizes goat.bb
column #10 isSizeLink do not match: Yours=[0]  BED Standard=[1]
asObjects differ

my goat.as file is:
table gene
"Genes for goat_new with Transcript and GeneSymbol"
(
string  chrom;  "Reference sequence chromosome or scaffold"
uint    chromStart;     "Start position of feature on chromosome"
uint    chromEnd;       "End position of feature on chromosome"
string  name;   "Name of transcript"
uint    score;  "Score"
char[1] strand; "+ or - for strand"
uint    thickStart;     "Coding region start"
uint    thickEnd;       "Coding region end"
uint    reserved;       "Blue on + strand, Red on - strand"
uint    blockCount;     "number"
string  blockSizes;     "Exon length"
string  blockStarts;    "Exon start"
string  geneSymbol;     "Gene Symbol"
)

I have attached my goat.bed.new.sorted file for your review. Please could you help me out here? Thank you very much for your time.

Kind regards,
Weiwei fu


 

goat.bed.new.sorted

Christopher Lee

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Jun 21, 2017, 12:56:19 PM6/21/17
to Fu weiwei, UCSC Genome Browser Discussion List
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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