Opened 13 years ago
Closed 13 years ago
#333 closed task (fixed)
Update to MeV 4.7
| Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
|---|---|---|---|
| Priority: | major | Milestone: | MeV Launcher v1.8 |
| Component: | net.sf.basedb.mev | Keywords: | |
| Cc: |
Description
They have added support for RNASeq data. Seems to be regular TDMS files with Count, RPKM or FPKM values. The existing TDMS exporter should be able to create the file already. The remaining question is what we have to do to tell MeV what is in the file. Can we do that with the java webstart parameters or can the user select it in the file dialog?
http://www.tm4.org/mev/?q=node/223 http://bioinformatics.oxfordjournals.org/content/early/2011/10/05/bioinformatics.btr490
Attachments (2)
Change History (4)
comment:1 by , 13 years ago
| Milestone: | MEV Launcher v1.x → MeV Launcher v1.8 |
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| Status: | new → assigned |
by , 13 years ago
| Attachment: | rnaseq-fpkm-loaded-as-tdms.png added |
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RNASeq FPKM data loaded with the TDMS file loader
comment:2 by , 13 years ago
| Resolution: | → fixed |
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| Status: | assigned → closed |
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I have upgraded to 4.7.3 and the FPKM data can be loaded if we use the "tdms" file loader. The "rnaseq" loader gives an error message about "Bad format error: Invalid File format for data type 0. Select valid format" (even when using one of the example RNASeq files from the MeV download). My guess is that the problem is that the "rnaseq" loader has several options in the file open dialog that can't be set from the command line (eg. Data Type, Species, Reference Genome, etc).
I'll move this ticket to 1.8 since it seems that the data can at least be loaded as "tdms". Don't know if downstream analysis will suffer from this or not.