Unable to visualize tracks for bw files in track hub for a custom species
Zhiwei Jiang
I have a bunch of bigwig files for Taeniopygia Guttata scATAC-seq and I want to visualize them in a track hub. I can create the track hub, but cannot get the tracks for bw files to show. Here is the files I used for the track hub:
1. hub.txt (url: https://data.cyverse.org/dav-anon/iplant/home/sebastianp/ZF_ATAC_zwjiang/RNA_anno_v1_bws/hub.txt)
hub ZebraFinchAuditoryForebrain
shortLabel zebra finch auditory forebrain scATAC-seq
longLabel zebra finch auditory forebrain scATAC-seq normalized accessibility in bigWig format
genomesFile genomes.txt
email zwj...@uchicago.edu
2. genomes.txt
genome GCF_003957565.2_bTaeGut1.4.pri
trackDb GCF_003957565.2_bTaeGut1.4.pri/trackDb.txt
twoBitPath GCF_003957565.2_bTaeGut1.4.pri/GCA_003957565.4_bTaeGut1.4.pri_genomic_refseq.2bit
organism Zebra Finch
scientificName Taeniopygia guttata
defaultPos NC_044219.2:14,322,322-14,348,470
3. GCF_003957565.2_bTaeGut1.4.pri/trackDb.txt (only the part for the first bw file)
track AST-1
bigDataUrl https://data.cyverse.org/dav-anon/iplant/home/sebastianp/ZF_ATAC_zwjiang/RNA_anno_v1_bws/GCF_003957565.2_bTaeGut1.4.pri/AST.1-TileSize-25-normMethod-ReadsInTSS-ArchR.bw
shortLabel AST-1
longLabel AST-1 scATAC-seq normalized read counts
type bigWig
priority 1
autoScale on
visibility full
4. GCF_003957565.2_bTaeGut1.4.pri/GCA_003957565.4_bTaeGut1.4.pri_genomic_refseq.2bit
Problems I have:
1. When feeding the url for hub.txt to the connected hubs url box, I can generate the track hub, but it is just for the GCF_003957565.2_bTaeGut1.4.pri genome view, and there are no tracks for my bw files.
2. The defaultPos is not directing the browser to the desired location of the genome.
Other behaviors I observed:
1. I can manually load the bw files using the ‘custom track’ at the browser view for the genome, and they can render correctly after that.
2. I am using refseq chromosome naming fashion in bw files and for the 2bit file.
I have been successful with creating human track hubs before also with bw files, but this time I failed for a custom species. Could anyone help me with this issue? Thanks!
Cheers,
Zhiwei
Jairo Navarro Gonzalez
Hello,
Thank you for using the UCSC Genome Browser and reporting your issues.
We are currently investigating why using your own genome definition is causing issues, but it may take a bit more time to find a solution. The problem appears to be that the UCSC Genome Browser uses the GenArk genome rather than your local definition.
The quickest solution is to use the GenArk genome in your hub instead of your local 2bit file. I have created the following hub.txt as an example, which also uses the "useOneFile on", so the hub contents are defined in one file instead of three:
https://hgwdev.gi.ucsc.edu/~jairo/MLQ/36545/hub.txt
Unfortunately, it does not appear that the defaultPos setting works for the track hub at the moment, and we have created an internal ticket to develop the feature. Out of curiosity, was this the reason you decided to host the genome assembly on your own server rather than using the GenArk assembly?
As a workaround for the default position, you can either create a session or use URL variables to view the correct location.
More information about using URL parameters can be found on the following help page:
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genome Browser
--
---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/9F387A1E-50D1-4014-B428-85D265A448C5%40uchicago.edu.