miRNAKey protocols

View miRNAKey computational protocol

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miRNAKey specifications

Information


Unique identifier OMICS_00364
Name miRNAKey
Software type Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format FASTA, FASTQ
Output data Differential expression table (excel table), summary report, plots of post-clipping read lengths, plots of multiple-alignment rates, clipped sequence files (adaptor clipped), mapped files and sequence files, separated to mapped and non-mapped reads.
Output format SAM, FASTQ, FASTA
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Requirements
Java, Burrows-Wheeler Alignment Tool, Fastx-Toolkit, the following Perl modules : Math, Spreadsheet, Getopt, GD
Maintained Yes

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Maintainers


  • person_outline Noam Shomron <>
  • person_outline miRNAKey Team <>

Additional information


http://ibis.tau.ac.il/miRNAkey/man.html

Publication for miRNAKey

miRNAKey in pipelines

 (6)
2017
PMCID: 5675615
PMID: 29152063
DOI: 10.18632/oncotarget.19693

[…] (illumina) that allows the identification of individual samples by “index sequences” contained within the adapters and introduced during the adapter ligation and amplification of the samples. mirnakey, was used for data analysis at default settings. the pipeline clips the illumina 3′ adaptor sequences, maps the clipped reads to mirbase and uses the seq-em algorithm to estimate […]

2016
PMCID: 4972903
PMID: 27454080
DOI: 10.1038/oncsis.2016.53

[…] (illumina) that allows the identification of individual samples by ‘index sequences' contained within the adapters and introduced during the adapter ligation and amplification of the samples. mirnakey was used for data analysis at default settings. the pipeline clips the illumina 3' adapter sequences from the reads, maps the clipped reads to mirbase and uses the seq-em algorithm […]

2016
PMCID: 5325330
PMID: 27588498
DOI: 10.18632/oncotarget.11716

[…] (illumina) that allows the identification of individual samples by “index sequences” contained within the adapters and introduced during the adapter ligation and amplification of the samples. mirnakey, a software package used for analyzing small rna data obtained from deep sequencing experiments, was used for data analysis at default settings. the pipeline clips the illumina 3′ adaptor […]

2014
PMCID: 4073505
PMID: 24942165
DOI: 10.1186/1471-2164-15-484

[…] sequences shorter than 16 nucleotides and adapter dimers. following adapter clipping, 8,340,741 and 9,441,679 reads remained. differential expression of the resulting sequences was performed using mirnakey. specifically, sequence alignment was performed using burrows-wheeler aligner (bwa) [] against mouse mature mirna sequences (downloaded from mirbase (release 20: june 2013; […]

2013
PMCID: 3585423
PMID: 23459507
DOI: 10.3389/fgene.2013.00020

[…] displayed. the cp value for each sequence in each sample are reported. the same total rna concentration was used for each sample. the probes for sequence 3 failed to amplify in any of the samples., mirnakey takes fastq sequencing files and aligns reads using bwa (li and durbin, ) to the relevant database, in our case mirbase 18. the software then can use an optional algorithm (seq-em) […]


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miRNAKey in publications

 (11)
PMCID: 5808213
PMID: 29467792
DOI: 10.3389/fgene.2018.00022

[…] with parameter setting should not overpower the treatment effect (such as the dose/time-dependent effect). in this study, four commonly used mirna-seq analysis tools (i.e., mirdeep2, mirexpress, mirnakey, srnabench) were comparatively evaluated with a standard toxicogenomics study design. we tested 30 different parameter settings on mirna-seq data generated from thioacetamide-treated rat […]

PMCID: 5675615
PMID: 29152063
DOI: 10.18632/oncotarget.19693

[…] formation has yet to occur (24 hours; a time when pax3 expression is gone but pax3-foxo1 is stable). the resulting sequencing data was analyzed in large-scale comparative mirna analyses using the mirnakey program (see materials and methods). the data used for subsequent analysis were limited to mirna displaying statistically significant differences (p < 0.05), as determined by the mirnakey […]

PMCID: 5352135
PMID: 27888798
DOI: 10.18632/oncotarget.13447

[…] and the ministry of health (0676-13-hmo)., rna of cell samples was extracted by tri-reagent. 1 μg of each sample was sequenced on an illumina genome analyzer []. data analysis was performed by a mirnakey application []., sh-scramble-plko.1 control plasmid, was described earlier []. mir-cnt plasmid refers to mir-k2 and sp-cnt plasmid refers to sp-ul112, they were provided by dr. dafna […]

PMCID: 5325330
PMID: 27588498
DOI: 10.18632/oncotarget.11716

[…] three independent growths of stably transduced primary myoblasts and utilized the resulting sequencing data in large-scale comparative transcriptomic analyses, using the on-line galaxy program or mirnakey, respectively (see materials and methods). since all stable lines were generated simultaneously and with identical methods, any artifactual effects of the process on mrna and mirna […]

PMCID: 4972903
PMID: 27454080
DOI: 10.1038/oncsis.2016.53

[…] the data used for subsequent studies were limited to (1) those genes or mirna displaying statistically significant differences (p<0.05, as determined by the galaxy cuffdiff program (mrna) or mirnakey (mirna)), (2) transcripts whose expression was present in both data sets being analyzed to rule out potential artifactual differences resulting from depth of read and (3) transcripts […]


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miRNAKey institution(s)
Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel; The Academic College of Tel-Aviv-Yaffo, Tel-Aviv, Israel; International Computer Science Institute, Berkeley, CA, USA; School of Computer Science and Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Science, Tel-Aviv University, Tel-Aviv, Israel
miRNAKey funding source(s)
Supported by Chief Scientist Office, Ministry of Health, Israel, The Kurz-Lion Foundation, The Tel Aviv University, Faculty of Medicine, Schreiber Foundation; The Wolfson Family Charitable Fund, Israeli Science Foundation (04514831), the National Science Foundation (IIS-071325412); Faculty fellow of the Edmond Safra Bioinformatics program at Tel-Aviv University, Edmond Safra Bioinformatics Program at Tel Aviv University and the Israeli Science Foundation (04514831).

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