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Download all hg19 coding sequences from UCSC

How to download all human coding sequences from UCSC table browser. The resulting format that we want to send to Galaxy is "gene ID, CDS in fasta".

human-genome galaxy cds
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updated by Ram Ram • written by Daniel • Daniel

1 answer

on the bash command line (assuming you have a mysql client installed):

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 \
-N -e 'SELECT * FROM knownGeneMrna' | sed -e 's/^/>/' -e 's/\s/\n/' > myFastaFile.fa

This will take a while to run. Make sure the output is what you want by sticking a LIMIT 10 in your SQL query:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 \
-N -e 'SELECT * FROM knownGeneMrna LIMIT 10' | sed -e 's/^/>/' -e 's/\s/\n/' > myFastaTestFile.fa
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updated by Ram Ram • written by Dan D Dan D

Thanks. Any way to do it through the table browser web interface?

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updated by Ram Ram • written by Daniel • Daniel

If you're willing to use the Ensembl annotation then you can just use Biomart.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

Doesn't this just download knownGeneMrna? These aren't just CDSs but include UTRs. Is there a way to get the CDS?

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updated by Ram Ram • written by jacobsen.jeremy • jacobsen.jeremy

There's a "coding sequence" option.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

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