Allowing track hubs to set chromosome aliases

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Hansen, Nancy (NIH/NHGRI) [E]

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Feb 14, 2024, 6:55:12 PM2/14/24
to gen...@soe.ucsc.edu

Hi again, Browser Team!

 

In the same context as my previous question (where I’m hosting a track hub built on GenArk assembly hubs), I’m now realizing how helpful it would be if my track hub could add chromosome aliases to the ones already present in each GenArk hub.

 

For our HG002 track hub, the aliases that GenArk has pulled from our NCBI submissions don’t include haplotype-specific names like “chr1_MATERNAL”, “chr3_PATERNAL”, etc., and many of the annotation files that our collaborators have generated are single data files (including both haplotypes) that use this naming scheme, which can help a lot in keeping track of which haplotype an entry is on. If I were able to specify a chromosome alias file in my genomes.txt file (e.g., something like “chromAliases\tmygenome/chromAliases.txt”), then I wouldn’t need to convert all these data files to UCSC’s naming scheme, and the users downloading the data files would have chromosome entry names that are the same as what the person who generated the data used.

 

Thanks for your attention,

--Nancy Hansen

 

-- 

*************************************

Nancy F. Hansen, PhD    nha...@mail.nih.gov

Staff Scientist, Genome Informatics Section

Computational and Statistical Genomics Branch (CSGB)

National Human Genome Research Institute (NHGRI)

National Institutes of Health (NIH)

49 Convent Drive, Rm 4A35

Bethesda, MD 20892

240-304-0362

 

 

 

 

 

Hiram Clawson

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Feb 15, 2024, 11:49:11 AM2/15/24
to Hansen, Nancy (NIH/NHGRI) [E], gen...@soe.ucsc.edu
Good Morning Nancy:

Can you please forward your chrom naming scheme for the two assemblies:

GCA_018852605.2_ASM1885260v2 human (NA24385 HG002 alt pat 2023)
GCA_018852615.2_ASM1885261v2 human (NA24385 HG002 pri mat 2023)

and I can drop that in place in our chromAlias files.

--Hiram

On 2/14/24 2:29 PM, 'Hansen, Nancy (NIH/NHGRI) [E]' via UCSC Genome Browser
Public Support wrote:
> Hi again, Browser Team!
>
> In the same context as my previous question (where I’m hosting a track hub built on GenArk assembly hubs), I’m now realizing how helpful it would be if my track hub could add chromosome aliases to the ones already present in each GenArk hub.
>
> For our HG002 track hub, the aliases that GenArk has pulled from our NCBI submissions don’t include haplotype-specific names like “chr1_MATERNAL”, “chr3_PATERNAL”, etc., and many of the annotation files that our collaborators have generated are single data files (including both haplotypes) that use this naming scheme, which can help a lot in keeping track of which haplotype an entry is on. If I were able to specify a chromosome alias file in my genomes.txt file (e.g., something like “chromAliases\tmygenome/chromAliases.txt”), then I wouldn’t need to convert all these data files to UCSC’s naming scheme, and the users downloading the data files would have chromosome entry names that are the same as what the person who generated the data used.
>
> Thanks for your attention,
> --Nancy Hansen
>
> --
> *************************************
> Nancy F. Hansen, PhD nha...@mail.nih.gov<mailto:nha...@mail.nih.gov>

Hansen, Nancy (NIH/NHGRI) [E]

unread,
Feb 15, 2024, 1:21:26 PM2/15/24
to Hiram Clawson, gen...@soe.ucsc.edu

Thanks so much, Hiram. Here are our aliases for the two assemblies. The first column is the Genbank accession, and it’s the *third* column--chr1, chr2, etc.—that we’d like to be the “ucsc” name, i.e. the name that will display given “chromAuthority ucsc”. If the hub could allow tracks to also have names from the 2nd or 4th column, that would be perfect for us:

 

For GCA_018852605.2

CP139534.1    Y      chrY   chrY_PATERNAL

CP139535.1    9      chr9   chr9_PATERNAL

CP139536.1    8      chr8   chr8_PATERNAL

CP139537.1    7      chr7   chr7_PATERNAL

CP139538.1    6      chr6   chr6_PATERNAL

CP139539.1    5      chr5   chr5_PATERNAL

CP139540.1    4      chr4   chr4_PATERNAL

CP139541.1    3      chr3   chr3_PATERNAL

CP139542.1    2      chr2   chr2_PATERNAL

CP139543.1    22     chr22  chr22_PATERNAL

CP139544.1    21     chr21  chr21_PATERNAL

CP139545.1    20     chr20  chr20_PATERNAL

CP139546.1    1      chr1   chr1_PATERNAL

CP139547.1    19     chr19  chr19_PATERNAL

CP139548.1    18     chr18  chr18_PATERNAL

CP139549.1    17     chr17  chr17_PATERNAL

CP139550.1    16     chr16  chr16_PATERNAL

CP139551.1    15     chr15  chr15_PATERNAL

CP139552.1    14     chr14  chr14_PATERNAL

CP139553.1    13     chr13  chr13_PATERNAL

CP139554.1    12     chr12  chr12_PATERNAL

CP139555.1    11     chr11  chr11_PATERNAL

CP139556.1    10     chr10  chr10_PATERNAL

For GCA_018852615.2

CP139510.1    MT     chrM   chrM_MATERNAL

CP139511.1    X      chrX   chrX_MATERNAL

CP139512.1    9      chr9   chr9_MATERNAL

CP139513.1    8      chr8   chr8_MATERNAL

CP139514.1    7      chr7   chr7_MATERNAL

CP139515.1    6      chr6   chr6_MATERNAL

CP139516.1    5      chr5   chr5_MATERNAL

CP139517.1    4      chr4   chr4_MATERNAL

CP139518.1    3      chr3   chr3_MATERNAL

CP139519.1    2      chr2   chr2_MATERNAL

CP139520.1    22     chr22  chr22_MATERNAL

CP139521.1    21     chr21  chr21_MATERNAL

CP139522.1    20     chr20  chr20_MATERNAL

CP139523.1    1      chr1   chr1_MATERNAL

CP139524.1    19     chr19  chr19_MATERNAL

CP139525.1    18     chr18  chr18_MATERNAL

CP139526.1    17     chr17  chr17_MATERNAL

CP139527.1    16     chr16  chr16_MATERNAL

CP139528.1    15     chr15  chr15_MATERNAL

CP139529.1    14     chr14  chr14_MATERNAL

CP139530.1    13     chr13  chr13_MATERNAL

CP139531.1    12     chr12  chr12_MATERNAL

CP139532.1    11     chr11  chr11_MATERNAL

CP139533.1    10     chr10  chr10_MATERNAL

 

 

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