Targetscan prediction locally

Question

[Soltani]

I am interested in using TargetScan locally on my computer, Anyone can help me how to do this ? thanks a lot

Answer 1

[rbagnall]

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.

[shashwatsahay.rsg]

Hey, How do we get to which version of mirbase they have used for this?