MiRTrans is a framework to incorporate trans-omics sequencing data to predict miRNA targets.
MicroRNA targets prediction by Trans-omics data
Input file(examples are in the ./input):
Four input files are required for detecting miRNA targets by MiRTrans，examples are in the ./input.
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Degradome sequencing: The raw sequencing data should be processed by Cleaveland4(http://sites.psu.edu/axtell/software/cleaveland4/). Three columns: miRNA name, transcript name and p-value with '\t' as delimiter.
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Sequence-based prediction: The union result combined from several sequence-based prediction software, such as PITA, TargetScan, psRNATarget etc. Two columns: miRNA name and transcript name with '\t' as delimiter.
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Transcript expression: The mRNA expression matrix as (m+1)*(n+1), where m is the number of mRNA and n is the sample size, with one row header and one column with mRNA name.
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MiRNA expresssion:The microRNA expression matrix as (m+1)*(n+1), where m is the number of microRNA and n is the sample size, with one row header and one column with microRNA name.
Run: python3 MiRTrans.py config1.txt The config1.txt is the configuration file with the path of inputs.