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GTEx human RNA-seq data analysis
- 1. Web portal for human APA outlier associated rare variants atlas A step-by-step guide
- 2. Data and methods • We collected RNA-seq data and WGS data from the v8 release of the GTEx project. The RNA-seq data contains 17,832 samples of 54 biological tissues from 838 donors. In the current study, we used 49 of the tissues that with at least 70 samples. Original RNA-seq reads were aligned with the human genome (hg38/GRCh38) using STAR v.2.5.2b. The resulting sorted BAM files were converted into bedGraph formats using BEDTools version 2.17.0 40. • We called APA outlier (aOutlier) in a single tissue (single-tissue aOutliers) and in multiple tissues (multitissue aOutliers). In brief, for multitissue aOutliers, we calculated the median Z score on covariates corrected APA usage for each APA event across all tissues for which data were available, restricting to individuals with APA measurements in at least five tissues. For each APA event, the multitissue aOutliers were defined as individuals with an absolute median value of Z score greater than 3. To account for situations where widespread aberrant APA might occur in an individual due to non-genetic influences, we removed 11 individuals where the proportion of tested genes that were multitissue outliers exceeded 1.5 times the interquartile range of the distribution of proportion outlier genes across all individuals. The 11 individuals were marked as global outliers. For single-tissue aOutlier calling, we calculated a Z score for each APA event and defined single-tissue aOutliers for each event in a single tissue as the individuals with the absolute value of Z score greater than 3. The 11 individuals marked as global outliers were also excluded in single-tissue aOutliers.
- 3. Part 1: Querying aOutliers/ipaOutliers of interest Part 2: Downloading data of aOutliers and the related data of the watershed model
- 4. Part 1 Querying aOutliers/ipaOutliers of interest Step 1: Search a Gene ( e.g. SUGP1)
- 5. Step 2: Select class of interest (e.g. 3’UTR)
- 6. Step 3: Relevant results will automatically show A search function is also available here.
- 7. Step 4: Click “Scatter plot ”
- 8. Step 5: Scatter plot for downloading
- 9. Part2 Downloading data of aOutliers and the related data of the watershed model Step 1: Click “DOWNLOAD”
- 10. Step 2: Click any filename for Visualizing and Downloading