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Dear Dr. Ou,
It seems that the interactive version of trackViewer can't handle negative values in bigWig files. Here is an example track in bigWig format: https://www.dropbox.com/s/efv612fw7b54xod/EpiK27me3Rep1.sub.bw?dl=0
I created the track by the following commands: bigwigCompare -b1 $f -b2 $f2 -o $out --scaleFactors 1:1 --operation subtract -v -p 4 --skipNonCoveredRegions
Is it possible for trackViewer to visualize IP-Input bigwig tracks
Thanks!
Ray
Hello Jianhong,
I'm helping biologists to use the web application of trackViewer, where we downloaded the docker image and started the GUI. I think we don't have the access to under-the-hood R objects from there.
Also, we had both positive and negative values in our bigWig files, and that represents the biological status that Pulldown sample is higher/lower than Input.
Is it possible to use the web application of trackViewer to visualize bigWig files with both positive and negative values? If it's not possible with the current version, would it be possible to have this capability in future versions?
Thanks!
Ray
Hello Jianhong,
I'm helping biologists to use the web application of trackViewer, where we downloaded the docker image and started the GUI. I think we don't have the access to under-the-hood R objects from there.
Also, we had both positive and negative values in our bigWig files, and that represents the biological status that Pulldown sample is higher/lower than Input.
Is it possible to use the web application of trackViewer to visualize bigWig files with both positive and negative values? If it's not possible with the current version, would it be possible to have this capability in future versions?
Thanks!
Ray
I will work on this soon.
Best!
Your sincerely,
Jianhong Ou
On Jul 31, 2019, at 11:27 AM, liruiradiant [bioc] <noreply@bioconductor.org<a rel="nofollow" href="mailto:noreply@bioconductor.org">noreply@bioconductor.org> wrote:
Activity on a post you are following on support.bioconductor.orghttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=5soCCQnCopTaM-hGehVU5ClLStwQTvPEzNuHhlfkMfM&s=EEAbgHHD80g90ErDXFvdz4bTMPkk9cnZjDDb1EpJdYo&e=
User liruiradianthttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_u_8906_&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=5soCCQnCopTaM-hGehVU5ClLStwQTvPEzNuHhlfkMfM&s=Oxhka4CJObuCsewAJoBwsVLk1G6WAMY_QidX3tGrl-U&e= wrote Comment: trackViewer, the interactive version, can't view negative values in bigWighttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_123342_-23123384&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=5soCCQnCopTaM-hGehVU5ClLStwQTvPEzNuHhlfkMfM&s=rWIPrtCMgl2ZG_rU0Oxb88d2JWjQoCFqnxX3jkdvxxI&e=:
Hello Jianhong,
I'm helping biologists to use the web application of trackViewer, where we downloaded the docker image and started the GUI. I think we don't have the access to under-the-hood R objects from there.
Also, we had both positive and negative values in our bigWig files, and that represents the biological status that Pulldown sample is higher/lower than Input.
Is it possible to use the web application of trackViewer to visualize bigWig files with both positive and negative values? If it's not possible with the current version, would it be possible to have this capability in future versions?
Thanks!
Ray
That is great. Thank you so much!!! Ray
Please have a try the newest docker. It should be OK to visualize the bw files with both positive and negative values.
Thanks a lot! I can visualize negative values now.
Thanks a lot! I can visualize negative values now.