Mus Musculus: Histone->Pluripotent Stem cells->mESC, differentiated database does not work

[mark0237]

Mus Musculus: Histone->Pluripotent Stem cells->mESC, differentiated database does not work. It is impossible to download nor view on the IGV. it shows an error message when trying to do it.

[shinyaoki]

Hi,

Thank you for the bug report. The error seems to be caused by the URL having comma (,), which will be fixed by the next update of ChIP-Atlas. You can instead visualize the genomic localization of "histones" in "mESC, differentiated" as follows:

1) Launch IGV and specify mm9 as a genome assembly. 2) File > Load from URL... 3) Enter following URL: http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.PSC.05.AllAg.mESCs,_differentiated.bed

Shinya

2020/06/09 6:10、mark0237 notifications@github.comのメール:

Mus Musculus: Histone->Pluripotent Stem cells->mESC, differentiated database does not work. It is impossible to download nor view on the IGV. it shows an error message when trying to do it.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/inutano/chip-atlas/issues/19, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADD2CTOSONBLGLAOILC3JATRVVHUHANCNFSM4NYYXXTA.

[mark0237]

thank you so much, it helped to view the whole set of experiments, but when i try to view the big wig file of a certain experiment, it has the same error. for example this one http://chip-atlas.org/view?id=SRX254804

how can i bypass the bug and view the big wig in these cases?

thank you

Lic. Marcos Gabriel Francia Profesor Adjunto - Universidad del Salvador Becario Doctoral - CONICET Laboratorio de Regulación Génica en Células Madre Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires. IQUIBICEN, CONICET-UBA. Intendente Guiraldes 2160 Ciudad Universitaria, Pab. 2, 4to piso, QB-71 C1428EGA, Buenos Aires Argentina tel: +54-11-5285-8683 fax: +54-11-4576-3342 marcos@qb.fcen.uba.ar

El lun., 8 de jun. de 2020 a la(s) 19:32, Shinya Oki ( notifications@github.com) escribió:

Hi,

Thank you for the bug report. The error seems to be caused by the URL having comma (,), which will be fixed by the next update of ChIP-Atlas. You can instead visualize the genomic localization of "histones" in "mESC, differentiated" as follows:

1) Launch IGV and specify mm9 as a genome assembly. 2) File > Load from URL... 3) Enter following URL:

http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.PSC.05.AllAg.mESCs,_differentiated.bed

Shinya

2020/06/09 6:10、mark0237 notifications@github.comのメール:

Mus Musculus: Histone->Pluripotent Stem cells->mESC, differentiated database does not work. It is impossible to download nor view on the IGV. it shows an error message when trying to do it.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/inutano/chip-atlas/issues/19>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ADD2CTOSONBLGLAOILC3JATRVVHUHANCNFSM4NYYXXTA .

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[shinyaoki]

Hi,

Apologies for my late reply. Upon clicking on "View on IGV" button in SRX254804 web page, ChIP-Atlas internally produce a following URL to load corresponding bigwig on IGV: http://localhost:60151/load?file=http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/eachData/bw/SRX254804.bw&genome=mm9&name=H3K27ac%20(@%20mESCs,%20differentiated)%20SRX254804

But, the URL is invalid because it includes a comma (,). To bypass this error: 1) Launch IGV. 2) File > Load from URL 3) Enter following URL: http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/eachData/bw/SRX254804.bw http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/eachData/bw/SRX254804.bw

This bug will be fixed by next update of ChIP-Atlas

Best, Shinya

2020/06/16 23:48、mark0237 notifications@github.comのメール:

thank you so much, it helped to view the whole set of experiments, but when i try to view the big wig file of a certain experiment, it has the same error. for example this one http://chip-atlas.org/view?id=SRX254804

how can i bypass the bug and view the big wig in these cases?

thank you

Lic. Marcos Gabriel Francia Profesor Adjunto - Universidad del Salvador Becario Doctoral - CONICET Laboratorio de Regulación Génica en Células Madre Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires. IQUIBICEN, CONICET-UBA. Intendente Guiraldes 2160 Ciudad Universitaria, Pab. 2, 4to piso, QB-71 C1428EGA, Buenos Aires Argentina tel: +54-11-5285-8683 fax: +54-11-4576-3342 marcos@qb.fcen.uba.ar

El lun., 8 de jun. de 2020 a la(s) 19:32, Shinya Oki ( notifications@github.com) escribió:

Hi,

Thank you for the bug report. The error seems to be caused by the URL having comma (,), which will be fixed by the next update of ChIP-Atlas. You can instead visualize the genomic localization of "histones" in "mESC, differentiated" as follows:

1) Launch IGV and specify mm9 as a genome assembly. 2) File > Load from URL... 3) Enter following URL:

http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.PSC.05.AllAg.mESCs,_differentiated.bed

Shinya

2020/06/09 6:10、mark0237 notifications@github.comのメール:

Mus Musculus: Histone->Pluripotent Stem cells->mESC, differentiated database does not work. It is impossible to download nor view on the IGV. it shows an error message when trying to do it.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/inutano/chip-atlas/issues/19>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ADD2CTOSONBLGLAOILC3JATRVVHUHANCNFSM4NYYXXTA .

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[inutano]

I'm closing this because the last update has already fixed this, let us know if you still have any problem with this @mark0237