trackViewer, the interactive version, can't view negative values in bigWig
1
0
Entering edit mode
@liruiradiant-8906
Last seen 21 months ago
United States

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 • 469 views
ADD COMMENT
1
Entering edit mode
Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
Last seen 21 days ago
United States

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 COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Thanks a lot! I can visualize negative values now.

ADD REPLY
0
Entering edit mode

Thanks a lot! I can visualize negative values now.

ADD REPLY

Login before adding your answer.

Traffic: 587 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6