Myrna

Cloud-scale differential gene expression for RNA-seq

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Related Tools

    Bowtie: Ultrafast short read alignment
    Crossbow: Cloud-scale genotyping
    Contrail: Cloud-based de novo assembly
    Hadoop: Open Source MapReduce
    Tophat: RNA-Seq splice junction mapper
    Cufflinks: Isoform assembly, quantitation

Reference jars

    H. sapiens GRCh37/Ensembl 67
     s3n://myrna-refs/human_ensembl_67.jar
     s3n://myrna-refs/human_ensembl_67.cs.jar (color)
    M. musculus NCBIM37/Ensembl 67
     s3n://myrna-refs/mouse_ensembl_67.jar
     s3n://myrna-refs/mouse_ensembl_67.cs.jar (color)
    P. troglodytes v2.1/Ensembl 67
     s3n://myrna-refs/chimp_ensembl_67.jar
     s3n://myrna-refs/chimp_ensembl_67.cs.jar (color)
    M. mulatta v1/Ensembl 67
     s3n://myrna-refs/rhesus_ensembl_67.jar
     s3n://myrna-refs/rhesus_ensembl_67.cs.jar (color)
    R. norvegicus RGSC3.4/Ensembl 67
     s3n://myrna-refs/rat_ensembl_67.jar
     s3n://myrna-refs/rat_ensembl_67.cs.jar (color)
    G. gallus WASHUC2/Ensembl 67
     s3n://myrna-refs/chicken_ensembl_67.jar
     s3n://myrna-refs/chicken_ensembl_67.cs.jar (color)
    C. familiaris BROADD2/Ensembl 67
     s3n://myrna-refs/dog_ensembl_67.jar
     s3n://myrna-refs/dog_ensembl_67.cs.jar (color)
    D. melanogaster BDGP5.13/Ensembl 67
     s3n://myrna-refs/fly_ensembl_67.jar
     s3n://myrna-refs/fly_ensembl_67.cs.jar (color)
    C. elegans WS210/Ensembl 67
     s3n://myrna-refs/worm_ensembl_67.jar
     s3n://myrna-refs/worm_ensembl_67.cs.jar (color)
    S. cerevisiae v1.01/Ensembl 67
     s3n://myrna-refs/yeast_ensembl_67.jar
     s3n://myrna-refs/yeast_ensembl_67.cs.jar (color)

Related publications

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Frequently Asked Questions

What's the difference between Myrna and (other tool)?

There are many tools that handle different aspects of analyzing RNA-seq data, but each tool usually has a specialty. Myrna's cloud mode and statistical models make it especially appropriate for very large datasets and datasets consisting of many biological replicates. Myrna's biggest drawback is that it does not attempt to align reads across junctions, assemble isoforms, or otherwise analyze on the isoform or junction level.

How do you say "Myrna"?

We say it like the first name Myrna ("mer nuh"). But you can say it however you want.

Does Myrna support colorspace?

Yes. All pre-built indexes (ending in .jar) have colorspace versions (ending in .cs.jar). Just be sure to specify the colorspace version of your reference jar of choice, and specify -C/--color among the options passed to Bowtie.

Can Myrna handle a mix of colorspace and normal (nucleotide-space) reads in a single job?

No. As of now, Myrna applies the same set of Bowtie arguments to every invocation of Bowtie, and so cannot be used on both types of reads in the same job.

Can I use Myrna to analyze an experiment with only one "group"

No. As of now, Myrna requires that the input be labeled such that there are at least two non-empty groups. Myrna will report per-gene differential expression p-values between these groups.

Why does my Myrna job fail in the statistics stage?

This is sometimes because the input consisted of just one group. See previous question.