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- Please cite: Langmead B, Hansen K, Leek J. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biology 11:R83.
- For release updates, subscribe to the mailing list.
| Myrna 1.1.2 | 5/25/11 |
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Related Tools
Reference jars
| H. sapiens GRCh37/Ensembl 58 |
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s3n://myrna-refs/human_ensembl_58.jar s3n://myrna-refs/human_ensembl_58.cs.jar (color) |
| M. musculus NCBIM37/Ensembl 58 |
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s3n://myrna-refs/mouse_ensembl_58.jar s3n://myrna-refs/mouse_ensembl_58.cs.jar (color) |
| P. troglodytes v2.1/Ensembl 58 |
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s3n://myrna-refs/chimp_ensembl_58.jar s3n://myrna-refs/chimp_ensembl_58.cs.jar (color) |
| M. mulatta v1/Ensembl 58 |
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s3n://myrna-refs/rhesus_ensembl_58.jar s3n://myrna-refs/rhesus_ensembl_58.cs.jar (color) |
| R. norvegicus RGSC3.4/Ensembl 58 |
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s3n://myrna-refs/rat_ensembl_58.jar s3n://myrna-refs/rat_ensembl_58.cs.jar (color) |
| G. gallus WASHUC2/Ensembl 58 |
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s3n://myrna-refs/chicken_ensembl_58.jar s3n://myrna-refs/chicken_ensembl_58.cs.jar (color) |
| C. familiaris BROADD2/Ensembl 58 |
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s3n://myrna-refs/dog_ensembl_58.jar s3n://myrna-refs/dog_ensembl_58.cs.jar (color) |
| D. melanogaster BDGP5.13/Ensembl 58 |
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s3n://myrna-refs/fly_ensembl_58.jar s3n://myrna-refs/fly_ensembl_58.cs.jar (color) |
| C. elegans WS210/Ensembl 58 |
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s3n://myrna-refs/worm_ensembl_58.jar s3n://myrna-refs/worm_ensembl_58.cs.jar (color) |
| S. cerevisiae v1.01/Ensembl 58 |
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s3n://myrna-refs/yeast_ensembl_58.jar s3n://myrna-refs/yeast_ensembl_58.cs.jar (color) |
Related publications
- Langmead B, Hansen K, Leek J. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biology 11:R83.
- Schatz M, Langmead B, Salzberg SL. Cloud computing and the DNA data race. Nature Biotechnology 2010 Jul;28(7):691-3.
- Langmead B, Schatz M, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biology 10:R134.
- Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
Authors
Links
Version 1.1.2 - May 23, 2011
- Updated jar files to use Ensembl v61 (used to be v58).
- Added --from-middle option that causes a read's overlap "influence" to be measured from the middle of the read rather than from one of the ends.
- Added --just-align and --resume-align options. --just-align causes Myrna to put the results of the Alignment phase in the --output directory and quit after the alignment phase. You can later "resume" Myrna by specifying this directory as the --input directory and specifying the --resume-align option.
- Fixed issue with .sra input whereby status output from fastq-dump would be interpreted as a read.
- Other minor bugfixes.
Version 1.1.1 - February 7, 2011
- Added support for the .sra file format, used by the Sequence Read Archive. These files can now be specified in the manifest. Crossbow uses the fastq-convert tool from the SRA Toolkit to convert .sra files to FASTQ files in the preprocess stage.
- The examples that included defunct SRA FASTQ files were updated to point to new .sra files instead.
- Fixed labeling scheme in $MYRNA_HOME/example/human/full.manifest to use proper format.
- Removed the --union-constitutive gene footprint which was effectively superseded by the --union-intersection footprint.
- Fixed issues with the Ensembl.pl/Ensembl.R scripts that would cause them to abort when no exons were marked as constitutive.
- Upgraded Bowtie version to 0.12.7.
Version 1.0.9 - September 13, 2010
- Fixed bug in cloud mode that would cause crashing in the Map portion of the Postprocess stage
- Fixed example manifests that point to Short Read Archive files to use .bz2 instead of .gz extensions.
Version 1.0.8 - September 4, 2010
- Set the memory cap on the sort task to be inversely proportional to --cpus, to avoid memory footprint blowup on computers with more processors.
- Fixed a final issue that affected how Myrna handles quality value conversion.
- Fixed issue whereby bzip2'ed data would be handled incorrectly by the preprocessor.
- Fixed counter in Preprocess step that would erroneously refer to unpaired reads as paired. Also "Read data fetched to EC2" has been changed to "Read data fetched".
- In EMR mode, updated where user credentials are found; Amazon changed their path sometime around 8/30/2010.
- In EMR mode, updated the manner in which the bootstrap action is specified; the old way was disabled by Amazon sometime around 8/30/2010.
- Fixed issue whereby ReduceWrap.pl would crash in cases with a large number of bins (>10 million) .
- NOTE: The Short Read Archive (SRA) seems to be in the midst of a reorganization that includes files that were previously gzipped being replaced with versions zipped with bzip2. The files will sometimes disappear for a while. If you are having problems with an example where input reads come from the SRA, try renaming files in the manifest file as appropriate. If that doesn't work, please contact us.
Version 1.0.7 - August 27, 2010
- Fixed issue whereby the order of the arguments to bowtie would result in a crash when POSIXLY_CORRECT was set.
- Fixed --keep-all option, which was causing a crash.
- Fixed a lingering quality bug whereby qualities were converted immediately to phred33 but phred64 or solexa64 flags would be spuriously passed to Bowtie.
Version 1.0.6 - August 26, 2010
- Single-computer mode now copies the output that it writes to the console to a file myrna.local.(pid).out. Please include the contents of this file when reporting issues.
- Sorting in single-computer mode is now more portable; switched from command-line sort to pure-Perl File::Sort.
- More helpful output from MapWrap.pl and ReduceWrap.pl to make it easier to debug issues in single-computer-mode runs.
- Fixed issue where web form would incorrectly convert + signs in AWS secret key to spaces, causing some good credentials to fail verification.
- Fixed issue in preprocessor that mishandles copies when user's AWS secret key contains slash characters.
Version 1.0.5 - August 16, 2010
- Fixed issue that prevented MYRNA_EMR_HOME environment variable from working.
- Fixed issue whereby Align.pl script fails to report a count for the number of reads with alignments sampled due to Bowtie's -M option.
- Fixed issue that made it difficult to specify a space-separated list of arguments to the --bowtie-args and other --*-args parameters.
- Fixed issue whereby most documentation referred to arguments with a single-dash prefix, whereas users with the POSIXLY_CORRECT environment variable set must use a double-dash prefix. Documentation and code have been updated to always use double-dash prefixes.
Myrna paper out - August 11, 2010
- The provisional version of the Myrna paper appeared today in Genome Biology.
Colorspace reference jars - July 30, 2010
- Added colorspace reference jars (see sidebar)
- Added Colorspace checkbox to the web interface to make it easy to specify a colorspace version of a pre-built reference jar
