How To Generate Bed File Only Containing The Cds Region ?

Question

[Zhilong Jia]

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.

Answer 1

[Sukhi Singh]

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

[Zhilong Jia]

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.