liftOver for genes which are moved to different chromosomes
maka...@mskcc.org
Good evening
I wonder if there is a way to deal with some genes when we translate between assemblies?
For example:
CD24:
chrY:21152526-21154705 - hg19
chr6:106969831-106975465 - hg38
When we translate from hg19 to hg38 coordinates, tools simply adds/subtracts values
https://www.ytree.net/hg19tohg38.html
It does not move genes between chromosomes.
Thus,
chrY:21152526-21154705
becomes
chrY:18990640-18992819
and not
chr6:106969831-106975465
Thank you very much,
Vlad
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Luis Nassar
Hello Vlad,
Thank you for your interest in the Genome Browser.
Our liftOver chains, which is what the liftOver program references, are based on whole-genome sequence alignments, and are filtered to include only the best alignment on the "from" genome (hg19 in this case). The best alignment of that part of hg19 chrY sequence is to hg38 chrY sequence, not chr6 sequence.
In the case of CD24, it is debatable whether is belonged on hg19 chrY to begin with. In hg19, it appears that chr6 was missing some sequence, and the best alignment of CD24 transcript sequence was to chrY. However, there is a fix patch for that part of chr6 in hg19 (and the fix was incorporated in hg38 chr6). If you click the following session link, you will see updated CD24 annotation on the chr6 fix sequence: http://genome-preview.soe.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=lou&hgS_otherUserSessionName=hg19CD24Fix
We are currently in the process of updating our liftOver chains, which should catch some of these cases.
In the meantime, a solution would be to query our data tables directly with the gene identifiers or gene symbols of interest. The coordinates you reference:
chrY:21152526-21154705 - hg19
chr6:106969831-106975465 - hg38
Correspond to a transcript with the accession NM_013230. If you go to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) and make the following selections:
Then, click on identifiers (names/accessions): and paste your list of identifiers (in this case NM_013230). Then get output and make these selections on the following screen: chrom txStart txEnd geneSymbol. Finally get output again. This will prompt a file download, and the file should look as follows:
You can vary the checked boxes if you would prefer more/less data. If you pass the CD24 gene symbol as the identifier instead of the specific transcript accession NM_013230, your output will include all the transcripts of the CD24 gene.
I hope this is helpful. If you have any further questions, please include gen...@soe.ucsc.edu in your reply to ensure visibility by the team. 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.
Lou Nassar
UCSC Genomics Institute
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maka...@mskcc.org
Good evening,
Thank you very much for your response.
Basically, if I tells us the hg38 coordinates of CD24 (which was on chrY in HG19)
chr6 106969830 106975465 CD24
My task is to convert not the whole gene coordinates, but enrichment peaks (bed file) with many regions.
It is a little off-topics, but I found an NCBI re-map tool
https://www.ncbi.nlm.nih.gov/genome/tools/remap
which provides conversion (result is practically the same as yours), but accept multiple peaks in bed format in hg19 and spits out their coordinates in hg38.
https://www.ncbi.nlm.nih.gov/genome/tools/remap/JSID_01_180209_130.14.18.128_9000_remap__1582339494
Would you recommend using it? It is slow, but seems to do right conversion.
Thank you
Vlad
From: Luis Nassar <lrna...@ucsc.edu>
Date: Friday, February 21, 2020 at 5:51 PM
To: "Makarov, Vladimir/Sloan Kettering Institute" <maka...@mskcc.org>
Cc: UCSC Genome Browser Discussion List <gen...@soe.ucsc.edu>
Subject: [EXTERNAL] Re: [genome] liftOver for genes which are moved to different chromosomes
Hello Vlad,
Thank you for your interest in the Genome Browser.
Our liftOver chains, which is what the liftOver program references, are based on whole-genome sequence alignments, and are filtered to include only the best alignment on the "from" genome (hg19 in this case). The best alignment of that part of hg19 chrY sequence is to hg38 chrY sequence, not chr6 sequence.
In the case of CD24, it is debatable whether is belonged on hg19 chrY to begin with. In hg19, it appears that chr6 was missing some sequence, and the best alignment of CD24 transcript sequence was to chrY. However, there is a fix patch for that part of chr6 in hg19 (and the fix was incorporated in hg38 chr6). If you click the following session link, you will see updated CD24 annotation on the chr6 fix sequence: http://genome-preview.soe.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=lou&hgS_otherUserSessionName=hg19CD24Fix
We are currently in the process of updating our liftOver chains, which should catch some of these cases.
In the meantime, a solution would be to query our data tables directly with the gene identifiers or gene symbols of interest. The coordinates you reference:
chrY:21152526-21154705 - hg19
chr6:106969831-106975465 - hg38
Correspond to a transcript with the accession NM_013230. If you go to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) and make the following selections:
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Matthew Speir
Matthew Speir
UCSC Genomics Institute
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/063429D7-88C3-4E94-9375-F00866EDB309%40mskcc.org.