How to generate bed file only containing the CDS region (such as in yeast) ?
that means the "name" field (the 4th field) in every line of bed file is a CDS region. Maybe UCSC table browser could work? But I really forget how to.
Thank you.
How to generate bed file only containing the CDS region (such as in yeast) ?
that means the "name" field (the 4th field) in every line of bed file is a CDS region. Maybe UCSC table browser could work? But I really forget how to.
Thank you.
This be it, you can use mysql
query [using S.cerevisae as an example]
mysql -B -h genome-mysql.cse.ucsc.edu -A -u genome -D sacCer3 -e 'select chrom,cdsStart,cdsEnd,name,proteinId,strand from sgdGene' | head
chrom cdsStart cdsEnd name proteinId strand
chrI 334 649 YAL069W n/a +
chrI 537 792 YAL068W-A n/a +
chrI 1806 2169 YAL068C P0CE93 -
chrI 2479 2707 YAL067W-A Q8TGK6 +
chrI 7234 9016 YAL067C P39709 -
chrI 10090 10399 YAL066W n/a +
chrI 11564 11951 YAL065C O13511 -
chrI 12045 12426 YAL064W-B O13512 +
chrI 13362 13743 YAL064C-A Q6B2U8 -
This will give you all the entries, though using table browser you can choose only to display the coding exons. May be some can add to the query
command how to do that.
or you can go to table browser,
Click the get bed.
Cheers
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yes, what I say is just your 2nd method. Thank you. When it comes to the former, I'm not familiar with mySQL. It seems just type the command in the local with the Internet connecting and then output the result.