UCSC chromosome names in T2T genome hub
Alexander Strunnikov
I started using the T2T human genome hub, and I noticed a weird bug: if I upload a simple bed file, it accepts UCSC chromosome names with no problems, but tracks in narrowPeak format do not recognize UCSC chromosome names and suggest NCBI names instead. Can it be fixed?
Thank you.
Alex
Luis Nassar
Hello, Alex.
Thank you for your interest in the Genome Browser.
Our chromAlias feature, which allows for annotations to be loaded with various sequence names, still has some cases that are being looked into such as the one you describe (using bed+ formats such as narrowPeak in conjunction with an assembly hub such as T2T).
While we are looking into fixing these issues, we have limited bandwidth and cannot offer a timeline for when that support will be expanded. In the meantime we offer two solutions:
1. We offer a utility (https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads), chromToUcsc, that can automatically convert most standard file formats including narrowPeak to UCSC convention chromosome names. You just need to point the utility to the appropriate chromAlias file, which for T2T would be here (https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.chromAlias.txt). Here is a direct link to the utility for linux: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/chromToUcsc
2. We are in the process of nativizing the CHM13-T2T assembly hub. This means that it will be a native Genome Browser assembly such as hg19 and hg38. One of the benefits of this would be that you should be able to upload your file with other sequence names and the chromAlias feature will automatically accept it. This adoption is currently under development and will be released soon, however, you can access it from our preview server here (http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=hs1). Keep in mind that not all data and features in our development server have undergone our QA process.
I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.
Lou Nassar
UCSC Genomics Institute
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