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  • 12:03
    tchannagiri commented #2064
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    cmdcolin on fix_sequence_panel

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    cmdcolin on fix_sequence_panel

    Fix issue with cDNA displays (compare)

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Jim Procter
@foreveremain:matrix.org
[m]
hey folks - does anyone have a successful recipe for building JBrowse2 on OSX/Big Sur (intel) ? I've stumbled through various native build hurdles and have a JBrowse2 electron app starting, but it fails to launch examples with 'TypeError: cannot read property of undefined'
2 replies
Colin Diesh
@cmdcolin
@foreveremain:matrix.org the issue with typeerror cannot read 'uri' of undefined may be fixed on the main branch if you pull the latest
the issue of librpc, it is not a private repo, it is just not on npm, but if it is causing issues we may want to fix that. You also should not need to add the node-sass install step so if you see an issue with that let us know
1 reply
Colin Diesh
@cmdcolin
Oh gotcha. I think we saw this node-sass issue on jbrowse 1 also using the latest node e.g. 15 or 16. Can downgrade to node 14 perhaps, but that could be worth fixing
6 replies
Colin Diesh
@cmdcolin
possible fix for the node-sass GMOD/jbrowse-components#2062
Kelsey Aadland
@kaadland
Hi there - I'm having a refName issue. When trying to load the genome view I get -- Error: Encountered invalid refName: "{". I've created an alias file for the chromosome names, and tried hard coding "refNameAliases" to the .json but I can't seem to get it to accept any change to the file. Any suggestions?
Garrett Stevens
@garrettjstevens
Hi @kaadland, it sounds like your alias file is a JSON file? JBrowse actually expects the aliases to be a tab-delimited file, for example: https://s3.amazonaws.com/jbrowse.org/genomes/hg19/hg19_aliases.txt
7 replies
HaoranLi
@li153348734
It seems that the cDNA bug has not been fixed. I downloaded the nightly version of jbrowse2, but the cDNA sequence above is inconsistent with the cDNA sequence I got. The length of the cDNA generated by jbrowse is shorter than the reference sequence. But the protein sequence and CDs sequence are correct.
Sometimes it grows longer. At this time, my reference sequence is only a part of the cDNA sequence generated by jbrowse.
HaoranLi
@li153348734
image.png
Starting from the red dot, all the following sequences are missing.
https://ngdc.cncb.ac.cn/gwh/Assembly/652/show This is where I download the data. You can download the data and add it to jbrowse2 after processing. The cDNA sequence provided by jbrowse is not consistent with that provided by the Tian.
Colin Diesh
@cmdcolin
@li153348734 thanks for reporting...ill check into it
HaoranLi
@li153348734
But in "jbrowse"_ In this version, the cDNA sequence is correct, because the bug I told you last time was only corrected in the test version. The bug I said last time is that if there is only one exon gene, its cDNA sequence is wrong. GMOD/jbrowse-components#2018
jbrowse create jbrowse_folder
this version the cdna sequence is right
You can try it on both versions
Colin Diesh
@cmdcolin
which versions?
gitter might have dropped the version numbers from your message due to markdown formatting or something
HaoranLi
@li153348734
image.png
this
HaoranLi
@li153348734
Its results are consistent with those provided by Tian
Hope to be helpful to the development of jbrowse2
Colin Diesh
@cmdcolin
really appreciate it :)
i will check into it
HaoranLi
@li153348734
Thank you. I'm in a bit of a hurry now, because my article will be submitted soon. Can I solve this problem as soon as possible?
Colin Diesh
@cmdcolin
you can also disable those sequence panels if there is interest, but i will try to fix also soon
HaoranLi
@li153348734
Thank you, but this function is very practical. If it is not easy to fix, I will ask you how to turn off this function :]
Scott Cain
@scottcain
I’ve been asked to lecture at the Programming for Biology course at CSHL this fall, so I need to start thinking about how to center around JB 2. If anybody has suggestions on what to cover, I’m all ears.
Colin Diesh
@cmdcolin
cool:) when is that course?
Scott Cain
@scottcain
Mid-October
Robin Haw
@hawrobin
Nice! it’s always nice to teach at CSHL. I just wish the journey from the airport to Cold Spring was a little quicker 😑
Scott Cain
@scottcain
In terms of topics, it seems like being more cancer focused than I usually am would be a good idea—I have a feeling that will be of more general interest.
Also, Sofia Robb (course organizer) asked about name searching (as does just about everybody I talk to :-) Any chance that will be in place by October?
HaoranLi
@li153348734
Hi! has this problem been solved?
@cmdcolin
HaoranLi
@li153348734
So how to disable cDNA? it's also very good that jbrowse can accept the FASTA file of cDNA cds and protein.
Colin Diesh
@cmdcolin
@li153348734 found a fix here GMOD/jbrowse-components@24dc8b4
you can use jbrowse create --nightly in about about 30 min and it will get the latest build with that fix
i agree that we'll probably want to add the ability to make it accept the fasta file of cdna and protein...issue to track here GMOD/jbrowse-components#2021
HaoranLi
@li153348734
Thank you! I will try now.
Colin Diesh
@cmdcolin
will take about ~30 min to be available on the --nightly build
HaoranLi
@li153348734
image.png
Okay, I got it
:]
Colin Diesh
@cmdcolin
no worry. the syntax is also jbrowse create --nightly foldername so that is what that message says
HaoranLi
@li153348734
uh huh, I'll try again in 30 minutes
HaoranLi
@li153348734
Great. This bug should have been fixed. I checked it and found no problem :]
Robert Buels
@rbuels
@scottcain yes text searching will definitely be in place by October