Question: trackViewer, the interactive version, can't view negative values in bigWig
0
gravatar for liruiradiant
3 months ago by
United States
liruiradiant0 wrote:

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

trackviewer • 145 views
ADD COMMENTlink modified 3 months ago by Ou, Jianhong1.2k • written 3 months ago by liruiradiant0
Answer: trackViewer, the interactive version, can't view negative values in bigWig
1
gravatar for Ou, Jianhong
3 months ago by
Ou, Jianhong1.2k
United States
Ou, Jianhong1.2k wrote:

Hi Ray,

You can put all the negative value into dat2 slot and convert the scores to positive.

Best!

Your sincerely,

Jianhong Ou

On Jul 30, 2019, at 7:48 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=EXqRF10Uz84gVHS3LxLIqnJBlANkor-tqJtbfI8kSO8&s=GCGE6ZsI6z-q0xPdZJrUyrJCN_jfompmp9CmQPs2lyY&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=EXqRF10Uz84gVHS3LxLIqnJBlANkor-tqJtbfI8kSO8&s=KhSr9k4lLsMrBdEjsIxQuzeb-geI8zbIyGQGY3D_Pxo&e= wrote Tutorial: trackViewer can't view negative values in bigWighttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_123342_&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=EXqRF10Uz84gVHS3LxLIqnJBlANkor-tqJtbfI8kSO8&s=HtADsXTYgVxpj0jwOTxmKV5xdUuMwoXZUHue73Bg5Q8&e=:

Dear Dr. Ou, it seems that trackViewer can't handle negative values in bigWig files. Here is an example track in bigWig format: https://www.dropbox.com/s/efv612fw7b54xod/Epihttps://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_efv612fw7b54xod_Epi&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=EXqRF10Uz84gVHS3LxLIqnJBlANkor-tqJtbfI8kSO8&s=9bV_LJUdRZGtZrEtkZRD2XE6s_BNd2OTESEZ0HaVxe4&e=K27me3Rep1.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

ADD COMMENTlink written 3 months ago by Ou, Jianhong1.2k

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

ADD REPLYlink written 3 months ago by liruiradiant0

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

ADD REPLYlink written 3 months ago by liruiradiant0

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

ADD REPLYlink written 3 months ago by Ou, Jianhong1.2k

That is great. Thank you so much!!! Ray

ADD REPLYlink written 3 months ago by liruiradiant0

Please have a try the newest docker. It should be OK to visualize the bw files with both positive and negative values.

ADD REPLYlink written 3 months ago by Ou, Jianhong1.2k

Thanks a lot! I can visualize negative values now.

ADD REPLYlink written 3 months ago by liruiradiant0

Thanks a lot! I can visualize negative values now.

ADD REPLYlink written 3 months ago by liruiradiant0
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