Entering edit mode
10.1 years ago
Soltani
▴
50
I am interested in using TargetScan locally on my computer, Anyone can help me how to do this ? thanks a lot
I am interested in using TargetScan locally on my computer, Anyone can help me how to do this ? thanks a lot
Hi,
You can download TargetScan (human) predictions from UCSC:
ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/targetScanS.txt.gz
Downloaded file looks like this:
591 chr1 879822 879830 SAMD11:miR-504 90 +
591 chr1 900599 900606 KLHL17:miR-299/299-3p 26 +
591 chr1 900605 900612 KLHL17:miR-124/506 7 +
591 chr1 900933 900941 KLHL17:miR-19 82 +
591 chr1 901054 901061 KLHL17:miR-137 14 +
592 chr1 990829 990836 AGRN:miR-144 10 +
592 chr1 990831 990838 AGRN:miR-27ab 47 +
592 chr1 990831 990838 AGRN:miR-128 16 +
592 chr1 990834 990841 AGRN:miR-224 50 +
A 3 column bed file; followed by gene:mirna; then score (1-100) of how well the reference sequence matches a predicted seed sequence; then strand (+ -) on which the sequence is found.
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Hey, How do we get to which version of mirbase they have used for this?