Download all hg19 coding sequences from UCSC
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8.4 years ago
Daniel ▴ 40

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 • 3.4k views
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8.4 years ago
Dan D 7.3k

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

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

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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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There's a "coding sequence" option.

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