Comments (11)
Hi,
Thank you for your interest in chimeraviz! Currently the package only supports the human genome (hg19 and hg38), but it would be interesting to improve chimeraviz to support other genomes as well. Is it only the mm10 genome you're interested in?
Note to self:
- mm10 cytoband data can be found here: http://hgdownload.cse.ucsc.edu/goldenpath/mm10/database/
- edb can be created with gtf file from here: ftp://ftp.ensembl.org/pub/release-74/gtf/mus_musculus/
- Also look at http://www.sanger.ac.uk/science/data/mouse-genomes-project
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Yes, mm10 is my current interest. Would that be possible that to guide the chimeraviz to read in the mm10 meta data, i.e., cytoband data, and do the visualization?
Thanks!
from chimeraviz.
Are you able to share your fusion finder results file, as well as a corresponding .bam file? That would help me add support for mm10 much faster :)
from chimeraviz.
from chimeraviz.
Great! If there are no unexpected problems then it won't take long for me to implement support for mm10 :)
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from chimeraviz.
If you can install chimeraviz from git now (with devtools::install_git("https://git.bioconductor.org/packages/chimeraviz.git")
), mm10 should work :) I've done some testing, but there might a couple of bugs I've missed. Please let me know about any issues you run into.
Note that this is the development version of chimeraviz. You might have to use a newer version of R, and newer versions of the supporting Bioconductor packages.
from chimeraviz.
from chimeraviz.
I'm sorry about that - it might've been because devtools::install_git
didn't install all the dependencies. The development version of chimeraviz (available at https://bioconductor.org/packages/devel/bioc/html/chimeraviz.html) has been updated to reflect yesterdays changes. So if you're able to install it from the instructions there, you should be good to go. Note however that the development version of Bioconductor is having some issues with CRAN packages on Windows at the moment, so it might not work for you if you're using Windows.
However, if you're able to work with Docker, I just tested it and that works. Dockerfile:
FROM bioconductor/devel_core2
RUN R -e 'source("https://bioconductor.org/biocLite.R");biocLite("chimeraviz")'
Build that with docker build . -t chimeravizDevBuild
(will take a few minutes). Then start with docker run -it -p 8787:8787 chimeravizDevBuild
. http://localhost:8787/ should then work:
The Bioconductor Docker images are built from the rocker:rstudio images, which give you the very nice Rstudio server.
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from chimeraviz.
That's great :) Do let me know how the mm10 support works for you. Just reopen this issue if there are any problems.
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Related Issues (20)
- Question: what are the red bands on the chromosome? HOT 4
- Assignment to global environment HOT 1
- plot_fusion function not finding "SPFQ" or "CADM2" transcripts in an edb object that has them. HOT 2
- Why is it impossible to use plot_fusion_transcript_with_protein_domain without a BAM file? HOT 1
- Support ChimPipe HOT 1
- coverage issue in plot_fusion_separate HOT 2
- How to make fusioncatcher data compatible to chimeraviz HOT 4
- Chromosome not labeled correctly? HOT 4
- Support Fusion-Bloom
- Travis build fails
- plot_fusion_transcript_with_protein_domain(): error plotting upstream domains HOT 2
- Failed to create reference fasta file HOT 4
- How to input STAR-SEQR output? HOT 1
- Dependency on deprecated ArgumentCheck CRAN package HOT 1
- 2 question with chimeraviz HOT 3
- Custom genomes HOT 2
- Error during the execution of plot_fusion HOT 5
- Failed to create EnsDb HOT 1
- No coverage data for plot_fusion HOT 2
- Fusion transcript plot with protein domain annotations HOT 1
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