| It's a flexible and very general implementation of a Bayesian approach to estimating Allelic Imbalance (AI) and formally comparing levels of AI between conditions. Allelic imbalance (AI) indicates the presence of functional variation in cis regulatory regions. Detecting cis regulatory differences using AI is widespread, yet there is no formal statistical methodology that tests whether AI differs between conditions. The testing for AI involves several complex bioinformatics steps. BayesASE is a complete bioinformatics pipeline that incorporates state-of-the-art error reduction techniques and a flexible Bayesian approach to estimating AI and formally comparing levels of AI between conditions (https://www.g3journal.org/content/8/2/447.long). |
hg clone https://testtoolshed.g2.bx.psu.edu/repos/malex/bayesase
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| merges filtered/summarized ASE Counts tables to the Calculated Prior values | 21.1.13 | 16.01 | |
| for one condition to test for Allelic Imbalance | 21.1.13 | 16.01 | |
| sum technical replicates | 21.1.13 | 16.01 | |
| - check read numbers in and out of Compare SAM Files and Create ASE Counts Tables tool | 21.1.13 | 16.01 | |
| for Bayesian Analysis of Allelic Imbalance | 21.1.13 | 16.01 | |
| that do not overlap with genic features for BayesASE (using awk) | 21.1.13 | 16.01 | |
| for correct formatting and duplicate FASTQ names | 21.1.13 | 16.01 | |
| containing read counts for each parental genome | 21.1.13 | 16.01 | |
| using ASE Count Tables | 21.1.13 | 16.01 | |
| for use in BayesASE Align and Count workflow | 21.1.13 | 16.01 | |
| verify starting FASTQ read number equals read number after running BWASplitSAM tool | 21.1.13 | 16.01 | |
| with awk | 21.1.13 | 16.01 | |
| for correct formatting and header names | 21.1.13 | 16.01 | |
| creates a SAM file of uniquely mapping reads from a BWA-MEM alignment | 21.1.13 | 16.01 | |
| based on user-defined APN threshold | 21.1.13 | 16.01 | |
| verify 2 SAM files are present for every 1 FASTQ file. | 21.1.13 | 16.01 | |
| with features of interest in RNAME field | 21.1.13 | 16.01 | |
| nbmodel_stan2_flex_prior.R | 21.1.13 | 16.01 | |
| converts a SAM file to a BED file for use in BayesASE | 21.1.13 | 16.01 | |
| for use in Calculate Priors Module for BayesASE | 21.1.13 | 16.01 | |