Author Topic: bed files in genome browser  (Read 4109 times)

incub0x

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bed files in genome browser
« on: April 07, 2016, 10:05:59 AM »
Hello:

I am using my bed files resulting in the tables of https://genome.ucsc.edu/cgi-bin/hgTables , with the next characteristics:


}group
~Genes and Gene Predictions

}region
~defined regions

#####  In this part, I uploaded a bed format file, in the first column of the bed format file is the chromosome, in the second column the beginning of the sequence, in the third column is the ending of the sequence and in the last column is the number of times that the sequence is in my file, for that reason, the fourth column is  very important to me. #####

}Output format
~selected fields from primary and related tables
~~~>get output.

~name
~chrom
~geneSymbol
~refseq
~description
~kgXref
~refSeqSummary
~~~>get output.


#### At the ending of the process the      genome.ucsc.edu      give me the chromosomes and the genes that correspond to the coordinates of the bed format file, but it doesn´t appear the fourth column next to the resulting genes. Some coordinates are not characterized, for that reason some coordinates are erased and I do not know what genes correspond to the specific number of the fourth column.


I would like to know if there is a way of getting the resulting genes with the numbers of the fourth column of my bed format file.

I would appreciate if someone can help me. ####


Thank you.

Alex

sjn

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Re: bed files in genome browser
« Reply #1 on: April 07, 2016, 10:19:10 AM »
Hi Alex,
I think your question would be better directed to the folks who maintain the UCSC Genome Browser.  Here is a good place to start: https://genome.ucsc.edu/contacts.html

BEDOPS doesn't have any internal knowledge about genes or other features but instead relies upon BED inputs that contain that information.  In your case, if the second file you describe had chromosome, start-of-sequence, end-of-sequence information and a Gene name in the fourth column, you could use BEDOPS to map the gene information onto your first file that contains the 4th column information that is important (# of times the sequence is found).  That's just one example.

Shane

incub0x

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Re: bed files in genome browser
« Reply #2 on: April 07, 2016, 10:33:53 AM »
Thank you very much for your help. This is useful for me.

 :) ;)