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TRECASE_MLE: eQTL Mapping based on Total Read Count and Allele-Specific Expression in RNA-Seq Data with Maximum-Likelihood Estimation  

2016-08-02 09:48:53|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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TRECASE_MLE is a command-line program written in C/C++ for eQTL mapping with RNA-seq data. TRECASE_MLE implemented the following steps in the five-step pipeline: (step 1) testing every local SNP for association with the expression of a gene and reporting the SNP with the minimum p-value (referred to as the minimum-p SNP) for each gene; (step 2) assessing the significance of every minimum-p SNP by a permutation process; (step 4) conducting the cis-trans test at every minimum-p SNP; and (step 5) estimating the effect size at every minimum-p SNP. All of these steps are performed for the TReC and TReCASE models in parallel. Note that Step 3 in the five-step pipeline that detects eQTLs among genome-wide minimum-p SNPs by FDR control can be performed using the R utility program “detect_eQTLs_byFDRcontrol.R” (provided in the zip file) based on the output of TRECASE_MLE; this R program generates the final list of detected eQTLs with determinedcis or trans mechanisms and estimated effect sizes. We are working intensely to improve the capabilities of TRECASE_MLE, so please check back frequently for updates.


To download TRECASE_MLE for 64-bit X86 based Linux, documentation, and an example dataset, please click here
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