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Protocols

FDM specifications

Information


Unique identifier OMICS_01332
Name FDM
Alternative name flow difference metric
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Input format SAM+GTF
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

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Publication for flow difference metric

FDM citations

 (3)
library_books

A survey of best practices for RNA seq data analysis

2016
Genome Biol
PMCID: 4728800
PMID: 26813401
DOI: 10.1186/s13059-016-0881-8

[…] r differences. By integrating the two steps, the uncertainty in the first step is taken into consideration when performing the statistical analysis to look for differential isoform expression []. The flow difference metric (FDM) uses aligned cumulative transcript graphs from mapped exon reads and junction reads to infer isoforms and the Jensen-Shannon divergence to measure the difference []. Recen […]

library_books

Comparisons of computational methods for differential alternative splicing detection using RNA seq in plant systems

2014
BMC Bioinformatics
PMCID: 4271460
PMID: 25511303
DOI: 10.1186/s12859-014-0364-4

[…] of programs is not exhaustive; however, we have selected a set of programs which represent a variety of approaches. Due to our limited human resources and computational power, the current versions of FDM [] and JuncBase [] met our criteria but were excluded from this study. FDM uses a splice graph representation of aligned RNA-seq data and Jensen Shannon Divergence (JSD) to measure the difference […]

call_split

Efficient experimental design and analysis strategies for the detection of differential expression using RNA Sequencing

2012
BMC Genomics
PMCID: 3560154
PMID: 22985019
DOI: 10.1186/1471-2164-13-484
call_split See protocol

[…] ecifically to appropriately handle expected technical and biological variation arising from RNA-Seq experiments. A non-exhaustive list of these algorithms is: edgeR [], DESeq [], NBPSeq [], BBSeq [], FDM [], RSEM [], NOISeq [], Myrna [], Cuffdiff []. A thorough comparison of these packages’ performance with datasets of different properties falls beyond the scope of this study, however before consi […]

Citations

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FDM institution(s)
Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Computer Science, University of Kentucky, Lexington, KY, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
FDM funding source(s)
Supported by National Science Foundation (ABI/EF grant number 0850237); National Institutes of Health: NCI TCGA (grant number CA143848); NCRR Idea (INBRE Grant P20RR016481); NCI GI SPORE Developmental Project Award (P50CA106991); Alfred P. Sloan Foundation fellowship.

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