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IDP-ASE specifications

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Unique identifier OMICS_14232
Name IDP-ASE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Raw genomic sequences for short read and long read data, a hybrid-Seq data in PSL alignment file, an annotation file (Genepred file in extended format), a list of biallelic/exonic SNPs in VCF format
Input format FASTQ
Biological technology Pacific Biosciences, Oxford Nanopore
Operating system Unix/Linux
License MIT License
Computer skills Advanced
Stability Stable
Requirements
julia, Bedtools, Mamba, ArgParse, Graphs, Distributions, StatsBase, Clustering
Maintained Yes

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Publication for IDP-ASE

IDP-ASE citations

 (2)
library_books

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis

2017
F1000Res
PMCID: 5553090
PMID: 28868132
DOI: 10.5256/f1000research.11392.r19894

[…] acBio or ONT alone, Hybrid-Seq can reduce the requirement of data size and improve the output, especially for transcriptome-wide studies. For example, a series of Hybrid-Seq methods (IDP, IDP-fusion, IDP-ASE) have been developed to improve the transcriptome studies to isoform levels (e.g., gene isoform reconstruction, fusion genes and allele phasing) with higher sensitivity and accuracy, and achie […]

call_split

IDP ASE: haplotyping and quantifying allele specific expression at the gene and gene isoform level by hybrid sequencing

2016
Nucleic Acids Res
PMCID: 5952581
PMID: 27899656
DOI: 10.1093/nar/gkw1076
call_split See protocol

[…] umina short reads, PacBio subreads and PacBio CCS reads. Below a concrete example of an error model is presented.Denote as the gene level relative ASE. Given the read data and the error, the goal of IDP-ASE is to obtain the most likely pair of haplotypes and the corresponding : Since is continuous and unknown, it will not be possible to enumerate all possibilities. Instead, samples from the join […]


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IDP-ASE institution(s)
Department of Biostatistics, University of Iowa, Iowa City, IA, USA; Department of Internal Medicine, University of Iowa, Iowa City, IA, USA; Key laboratory of Genetics Network Biology, Collaborative Innovation Center of Genetics and Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
IDP-ASE funding source(s)
Supported by the National Human GenomeResearch Institute (R01HG008759); the Multidisciplinary Lung Research Career Development Program (T32HL007638); the Presidential Graduate Research Fellowship, University of Iowa; the National Natural Science Foundation of China (No. 91540204) and the institutional fund of Department of Internal Medicine, University of Iowa.

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