This is an easily-to-use tool for users to predict human osteoblast-specific target genes of human miRNA of interest. The TargetScan v7.2 and miRDB v6.0 are jointly used to form a putative targets pool with the given thresholds, the AGO2 CLIP-seq data is used to fliter false postive targets. User could just input a list of miRNA in local.
Use the follow command to download:
$ git clone https://github.com/WeiYang-BAI/Osteo-miRNA-Target-Prediction-Tool.git
The miRDB data used in the tool was gziped, please unzip it before use:
$ cd data
$ gunzip miRDB_v6.0_hsaOnly.txt.gz
Run the follow command to see the help message:
$ cd ..
$ python ./miRNA_Target_Prediction.py -H
Arguments:
-H/-h Show this help-doc.
-miRNA The miRNAs list file , one miRNA per line. Please use the complete miRNA name,
e.g. hsa-miR-218-5p.
[-tarScanScore] Optional. The threshold of cumulative weighted context++ score in
TargetScan v7.2 to filter results. The predicted target with the score
great than this threshold will be filtered out. The value range is [-1, 0]
(-1 means best prediction). The defult value is -0.2.
[-miRDBScore] Optional. The threshold for prediction confidence in miRDB-V6.0 to filter
results. The predicted target with the score lower than this threshold will
be filtered out. The value range is [50, 100] (100 means best prediction).
The defult value is 60.
-outputDir A folder will be used to store results.
An example is given, run it in the command line for details:
$ sh example.sh
Output folder/files into -outputDir:
TargetScan_v7.2/TarScan-miRNA.tsv, prediction of TargetScan results.
miRDB_v6.0/miRDB_NM-miRNA.tsv, prediction of miRDB results.
final_targets/Targets-miRNA.tsv, the union of TargetScan and miRDB results, and filterd by AGO2 CLIP-seq data.