Mus Musculus: Histone->Pluripotent Stem cells->mESC, differentiated database does not work
Closed this issue · 4 comments
mark0237 commented
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 commented
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 ***@***.***>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 <#19>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADD2CTOSONBLGLAOILC3JATRVVHUHANCNFSM4NYYXXTA>.
mark0237 commented
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 ***@***.***>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 <
#19>, or unsubscribe <
https://github.com/notifications/unsubscribe-auth/ADD2CTOSONBLGLAOILC3JATRVVHUHANCNFSM4NYYXXTA
>.
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#19 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/APXXLEPBIW3QG4UCOOA7JNTRVVRJJANCNFSM4NYYXXTA>
.
shinyaoki commented
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 ***@***.***>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
***@***.***
El lun., 8 de jun. de 2020 a la(s) 19:32, Shinya Oki (
***@***.***) 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 ***@***.***>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 <
> #19>, or unsubscribe <
> https://github.com/notifications/unsubscribe-auth/ADD2CTOSONBLGLAOILC3JATRVVHUHANCNFSM4NYYXXTA
> >.
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#19 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/APXXLEPBIW3QG4UCOOA7JNTRVVRJJANCNFSM4NYYXXTA>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub <#19 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADD2CTMT4ILUAYW5OUTXA3TRW6A4TANCNFSM4NYYXXTA>.