Myrna protocols

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chevron_left Read alignment Differential expression Known transcript quantification Differential abundant feature detection Normalization Bioinformatics workflows chevron_right
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Myrna specifications

Information


Unique identifier OMICS_01310
Name Myrna
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Parallelization MapReduce
Computer skills Advanced
Version 1.2.3
Stability Stable
High performance computing Yes
Maintained Yes

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Maintainer


  • person_outline Jeffrey Leek <>

Publication for Myrna

Myrna in pipelines

 (2)
2013
PMCID: 3655485
PMID: 23710461
DOI: 10.1155/2013/791051

[…] available in the aws website []. , currently, there are some cloud-based programs for the analysis of next-generation sequencing data. these include, among others, crossbow [], rsd-cloud [], myrna [], and cloudburst []. in addition, there are some libraries and packages that support the creation and management of computer clusters in the cloud. to the best of our knowledge, these include […]

2013
PMCID: 3655485
PMID: 23710461
DOI: 10.1155/2013/791051

[…] various bioinformatics programs are already based on the mapreduce framework and are demonstrated to work using the emr product. examples of these tools include crossbow [], rsd-cloud [], myrna [], and cloudburst []., the client program of elastream can create an emr cluster using the apis of aws from the user's local machine. the creation steps are similar to that of the traditional […]


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Myrna in publications

 (10)
PMCID: 5875741
PMID: 29596416
DOI: 10.1371/journal.pcbi.1005994

[…] developer burden and provides a technologically advanced solution that need not be reinvented., an example of a cloud-based biomedical informatics workflow which benefits from managed services is myrna, which is a pipeline for alignment of rna-seq reads and investigation of differential transcript expression []. myrna utilizes elastic mapreduce (emr), a managed hadoop service offered […]

PMCID: 5537105
PMID: 28794828
DOI: 10.1016/j.csbj.2017.07.002

[…] aligner (bwa), and a reduce step, which performs variant calling in a chromosomal region using genome analysis toolkit (gatk). other examples of mapreduce-based bioinformatics analysis tools include myrna, which performs rna-sequencing gene expression analysis and cloudaligner, a short-read sequence aligner.fig. 2fig. 2., one disadvantage of the mapreduce programming model is the need […]

PMCID: 4631466
PMID: 26539333
DOI: 10.7717/peerj.1360

[…] identified two suitable rna-seq data sets in the recount database (). the latter contains unnormalized rna-seq count data sets from 18 major studies that have been assembled from raw reads using the myrna () pipeline., the bottomly data set () consists of gene expression data (22 million illumina reads per sample, read length of ∼30 bases) obtained from the brain striatum tissues of two mice […]

PMCID: 4222140
PMID: 25414713
DOI: 10.3389/fpls.2014.00599

[…] different samples and a contingency table with contig names was created using the number of reads per reference contig per sample. the contingency table was normalized at a 95 percentile using the myrna (langmead et al., ) statistical analysis package and the differential gene expression was evaluated using a linear regression model based on a gaussian distribution and taking into account […]

PMCID: 3881492
PMID: 24314033
DOI: 10.1186/1471-2105-14-358

[…] system–the “disk” that mapreduce utilizes. both inspired open-source counterparts that compose the core apache hadoop project: hadoop mapreduce and the hadoop distributed file system (hdfs) []., myrna[] applies hadoop mapreduce to the analysis of rna-seq data, using hadoop to count the unique alignments in an experiment. the map phase iterates through the alignments, emitting a tuple […]


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Myrna institution(s)
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA

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