Visualization of chimeric transcript from Non-human organism

[wyzhangMPI]

Hi, I would like to know whether chimeraviz can be used for the visualization of the chimeric transcript from non-human organims. I tried import the fusion data with "fusions <- importStarfusion(defuse833ke, "mm10")", but failed with genome version info.

Thanks!

Best, Wenyu Zhang

[stianlagstad]

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

[wyzhangMPI]

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!

[stianlagstad]

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 :)

[wyzhangMPI]

Hi, I will upload the dataset to our ftp server tomorrow and provide you the link then. Thanks!

Best, Wenyu

Original Message Sender:Stian Lågstadnotifications@github.com Recipient:stianlagstad/chimeravizchimeraviz@noreply.github.com Cc:wyzhangMPIwyzhang@evolbio.mpg.de; Authorauthor@noreply.github.com Date:Tuesday, Nov 28, 2017 18:29 Subject:Re: [stianlagstad/chimeraviz] Visualization of chimeric transcriptfrom Non-human organism (#14)

Are you able to share your fusion finder results file, as well as the corresponding .bam file? That would help me add support for mm10 much faster :) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[stianlagstad]

Great! If there are no unexpected problems then it won't take long for me to implement support for mm10 :)

[wyzhangMPI]

Hi, I upload all the data from the output of star-fusion: http://web.evolbio.mpg.de/~wyzhang/Webdav_Pub/star_fusion_outdir/. You can find the tsv and bam file there. Look forward to seeing that chimeraviz works on mm10. Thanks!

Best, Wenyu

Dr Wenyu Zhang Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology August-Thienemann-str 2 24306 Plön (Germany) E-mail address: wyzhang@evolbio.mpg.de Phone number: +49 4522 763 372 (Office)

------ Original Message ------ From: "Stian Lågstad" notifications@github.com To: "stianlagstad/chimeraviz" chimeraviz@noreply.github.com Cc: "wyzhangMPI" wyzhang@evolbio.mpg.de; "Author" author@noreply.github.com Sent: 11/28/2017 6:48:47 PM Subject: Re: [stianlagstad/chimeraviz] Visualization of chimeric transcript from Non-human organism (#14)

Great! If there are no unexpected problems then it won't take long for me to implement support for mm10 :)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/stianlagstad/chimeraviz/issues/14#issuecomment-347606086, or mute the thread https://github.com/notifications/unsubscribe-auth/AbjeYJSWgq6hSj4Ie7dLgtPb_Or8a3Smks5s7Ed-gaJpZM4QtOf3.

[stianlagstad]

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.

[wyzhangMPI]

Hi, I tried with newest R version, and it seems that works well. I will let you know if any further issues. Thanks so much!

[stianlagstad]

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.

[wyzhangMPI]

Hi, Sorry, I just updated my comments. I manually downloaded org.Mm.eg.db through bioconductor, and now it works well. Thanks!

Best, Wenyu

------ Original Message ------ From: "Stian Lågstad" notifications@github.com To: "stianlagstad/chimeraviz" chimeraviz@noreply.github.com Cc: "wyzhangMPI" wyzhang@evolbio.mpg.de; "Author" author@noreply.github.com Sent: 12/1/2017 3:11:10 PM Subject: Re: [stianlagstad/chimeraviz] Visualization of chimeric transcript from Non-human organism (#14)

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: https://user-images.githubusercontent.com/4340859/33486312-d786d0b2-d6a9-11e7-9e99-94de2df176db.png

The Bioconductor Docker images https://www.bioconductor.org/help/docker/ are built from the rocker:rstudio images https://hub.docker.com/r/rocker/rstudio/, which gives you the very nice Rstudio server.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/stianlagstad/chimeraviz/issues/14#issuecomment-348504076, or mute the thread https://github.com/notifications/unsubscribe-auth/AbjeYEn89BOlOL-Tdo9QfljvS7HMjqFsks5s8Aj-gaJpZM4QtOf3.

[stianlagstad]

That's great :) Do let me know how the mm10 support works for you. Just reopen this issue if there are any problems.