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谭弄璋, Jairo Navarro Gonzalez2

Mar 13

Request for hg38-to-Other-Species liftOver Chain Files (Multiz 470-way Alignment)

generate the liftOver files that are needed for your project. I have started the alignment between hg38 and GCF_000956065.1 (Mnem_1.0/macNem1) and will let you know when it is available

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Request for hg38-to-Other-Species liftOver Chain Files (Multiz 470-way Alignment)

generate the liftOver files that are needed for your project. I have started the alignment between hg38 and GCF_000956065.1 (Mnem_1.0/macNem1) and will let you know when it is available

Mar 13

Abigail Sequeira, Luis Nassar2

Mar 2

LiftOver chain file from human hg18 to T2T-PanTro

The requested liftOver file can now be found here: https://hgdownload.gi.ucsc.edu/goldenPath/hg18/liftOver/hg18ToGCF_028858775.2.over.chain.gz On Fri, Feb 13, 2026 at

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LiftOver chain file from human hg18 to T2T-PanTro

The requested liftOver file can now be found here: https://hgdownload.gi.ucsc.edu/goldenPath/hg18/liftOver/hg18ToGCF_028858775.2.over.chain.gz On Fri, Feb 13, 2026 at

Mar 2

Batra, Sajeev, Gerardo Perez2

Feb 17

dbsnp RSIDs on canFam6

to use LiftOver to convert SNPs between two assembly versions. Using LiftOver to convert a very small region, especially a single-base SNP, is not always a trivial task, as the alignment

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dbsnp RSIDs on canFam6

to use LiftOver to convert SNPs between two assembly versions. Using LiftOver to convert a very small region, especially a single-base SNP, is not always a trivial task, as the alignment

Feb 17

Jonathan Sulc, Jairo Navarro Gonzalez3

Jan 30

Liftover from hg38 to hg18

genome] Liftover from hg38 to hg18 Hello, Thank you for using the UCSC Genome Browser and sending your inquiry. These liftOver files are now available for download and can be obtained

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Liftover from hg38 to hg18

genome] Liftover from hg38 to hg18 Hello, Thank you for using the UCSC Genome Browser and sending your inquiry. These liftOver files are now available for download and can be obtained

Jan 30

Lankinen, Teemu X, Gerardo Perez3

Jan 26

FW: over.chain file request

hg19/liftOver/hg19ToHg38.over.chain.gz https://hgdownload.gi.ucsc.edu/goldenpath/hg38/liftOver/hg38ToHg19.over.chain.gz I hope this is helpful. If you have any further

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FW: over.chain file request

hg19/liftOver/hg19ToHg38.over.chain.gz https://hgdownload.gi.ucsc.edu/goldenpath/hg38/liftOver/hg38ToHg19.over.chain.gz I hope this is helpful. If you have any further

Jan 26

Manoj Hariharan, … Hiram Clawson14

Jan 23

Liftover mm10 to CBAJ mouse

The 'liftOver' command with the 'over.chain.gz' file will require your input to be in the same name space as in the 'over.chain.gz' file. The alignment

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Liftover mm10 to CBAJ mouse

The 'liftOver' command with the 'over.chain.gz' file will require your input to be in the same name space as in the 'over.chain.gz' file. The alignment

Jan 23

Chen Lou, Gerardo Perez2

Jan 15

Clarifying the Meaning of Coordinates, Strand, and Score in BED Files and liftover Results

after running LiftOver, this is a bug. The score value should remain the same after LiftOver. We have created an internal ticket to address this issue, but we are not able to provide an

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Clarifying the Meaning of Coordinates, Strand, and Score in BED Files and liftover Results

after running LiftOver, this is a bug. The score value should remain the same after LiftOver. We have created an internal ticket to address this issue, but we are not able to provide an

Jan 15

Nathani, Kaizen, Luis Nassar2

Jan 6

Liftover chain file for hg19 to hg38

to hg38 liftOver file can be found on our download server here: https://hgdownload.gi.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz On Tue, Jan 6, 2026 at 12

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Liftover chain file for hg19 to hg38

to hg38 liftOver file can be found on our download server here: https://hgdownload.gi.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz On Tue, Jan 6, 2026 at 12

Jan 6

Lin Ou, Luis Nassar6

12/8/25

Request for chain files of different tree shrew genome version

1/liftOver/GCA_033439345.1ToTupBel1.over.chain.gz https://hgdownload.gi.ucsc.edu/goldenPath/tupBel1/liftOver/tupBel1ToGCA_033439345.1.over.chain.gz On Wed

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Request for chain files of different tree shrew genome version

1/liftOver/GCA_033439345.1ToTupBel1.over.chain.gz https://hgdownload.gi.ucsc.edu/goldenPath/tupBel1/liftOver/tupBel1ToGCA_033439345.1.over.chain.gz On Wed

12/8/25

Jillian Ness, Gerardo Perez2

12/4/25

dm6 genome coordinates to musDom2 genome

the requested liftOver chain files available on our download server: dm6 -> musDom2: https://hgdownload.soe.ucsc.edu/goldenPath/dm6/liftOver/dm6ToMusDom2.over.chain

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dm6 genome coordinates to musDom2 genome

the requested liftOver chain files available on our download server: dm6 -> musDom2: https://hgdownload.soe.ucsc.edu/goldenPath/dm6/liftOver/dm6ToMusDom2.over.chain

12/4/25

Yusuke Kishi, Matthew Speir3

12/4/25

LiftOver for from mm10 to CalJac1

request for LiftOver files. These files are now available on our download server: > https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToCalJac1.over.chain

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LiftOver for from mm10 to CalJac1

request for LiftOver files. These files are now available on our download server: > https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToCalJac1.over.chain

12/4/25

狄艳, Jairo Navarro Gonzalez2

11/26/25

Request for liftOver chain files

1/liftOver/GCF_964237555.1ToGCF_016772045.1.over.chain.gz Rabbit to Cattle: https://hgdownload.soe.ucsc.edu/hubs/GCF/964/237/555/GCF_964237555.1/liftOver/GCF_964237555

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Request for liftOver chain files

1/liftOver/GCF_964237555.1ToGCF_016772045.1.over.chain.gz Rabbit to Cattle: https://hgdownload.soe.ucsc.edu/hubs/GCF/964/237/555/GCF_964237555.1/liftOver/GCF_964237555

11/26/25

Lin Ou, Gerardo Perez4

11/10/25

Request for multiple alignment file and phastCons scores with new tree shrew and rabbit genome

hg38/liftOver/ > https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/ > https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/liftOver/ > > https

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Request for multiple alignment file and phastCons scores with new tree shrew and rabbit genome

hg38/liftOver/ > https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/ > https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/liftOver/ > > https

11/10/25

jelly_12321, Luis Nassar3

10/31/25

Request for Chain File

susScr11/liftOver/susScr11ToGCF_016772045.2.over.chain.gz On Fri, Oct 24, 2025 at 12:54 PM Luis Nassar wrote: > Hi, Jelly. > > We can generate that chain file for you

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Request for Chain File

susScr11/liftOver/susScr11ToGCF_016772045.2.over.chain.gz On Fri, Oct 24, 2025 at 12:54 PM Luis Nassar wrote: > Hi, Jelly. > > We can generate that chain file for you

10/31/25

周亚琦, … Gerardo Perez4

10/30/25

USCS LiftOver Queries

the requested liftOver chain files available on our download server: pig (susScr11) to blue whale (GCF_009873245.2): https://hgdownload.soe.ucsc.edu/goldenPath/susScr11

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USCS LiftOver Queries

the requested liftOver chain files available on our download server: pig (susScr11) to blue whale (GCF_009873245.2): https://hgdownload.soe.ucsc.edu/goldenPath/susScr11

10/30/25

Chengcheng Song, Jairo Navarro Gonzalez4

10/28/25

About canFam2 to canFam4 chain file

requesting your liftOver files. The alignments have now finished, and the liftOver files are available for download: canFam2 to canFam4: https://hgdownload.soe.ucsc.edu/goldenPath

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About canFam2 to canFam4 chain file

requesting your liftOver files. The alignments have now finished, and the liftOver files are available for download: canFam2 to canFam4: https://hgdownload.soe.ucsc.edu/goldenPath

10/28/25

许晋升, Gerardo Perez2

10/27/25

Request for liftOver chain files

The requested liftOver files can be found on our download server: ROS_Cfam_1.0 (GCF_014441545.1) to canFam6: https://hgdownload.soe.ucsc.edu/hubs/GCF/014/441/545/GCF_014441545

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Request for liftOver chain files

The requested liftOver files can be found on our download server: ROS_Cfam_1.0 (GCF_014441545.1) to canFam6: https://hgdownload.soe.ucsc.edu/hubs/GCF/014/441/545/GCF_014441545

10/27/25

Kori_C...@eisai.com, Luis Nassar2

10/24/25

Error While Running Liftover in Docker Image

using the liftOver binary from our v479 freeze ( https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v479/), which may work. On Fri, Oct 10, 2025 at 12:32 PM Kori_Clermont

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Error While Running Liftover in Docker Image

using the liftOver binary from our v479 freeze ( https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v479/), which may work. On Fri, Oct 10, 2025 at 12:32 PM Kori_Clermont

10/24/25

和士杰, Jairo Navarro Gonzalez2

10/24/25

Subject: Chain file request

requesting these liftOver files. The alignments have now finished and are available for download: Mouse to Blue whale: https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver

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Subject: Chain file request

requesting these liftOver files. The alignments have now finished and are available for download: Mouse to Blue whale: https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver

10/24/25

Lin Ou, … Gerardo Perez10

10/20/25

LiftOver chain files for new version tree shrew genome and rabbit genome to human genome conversions

the requested liftOver chain files available on our download > server: > > rabbit(GCA_013371645.1) to mouse(mm10): > https://hgdownload.soe.ucsc.edu/hubs/GCA

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LiftOver chain files for new version tree shrew genome and rabbit genome to human genome conversions

the requested liftOver chain files available on our download > server: > > rabbit(GCA_013371645.1) to mouse(mm10): > https://hgdownload.soe.ucsc.edu/hubs/GCA

10/20/25

Peiyuan Zhu, Jairo Navarro Gonzalez2

10/17/25

Strand designation issue

input, LiftOver will use and respect the strand if specified as the 4th column. However, if no strand column is supplied, or the strand is ".", then Liftover defaults to the

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Strand designation issue

input, LiftOver will use and respect the strand if specified as the 4th column. However, if no strand column is supplied, or the strand is ".", then Liftover defaults to the

10/17/25

Peiyuan Zhu, Clay Fischer2

10/15/25

Data format error: expecting at least 3 fields in BED file

use of liftOver with a PLINK BED file. A PLINK BED file is not the same thing as a UCSC BED (Browser Extensible Data) file. You can review the UCSC BED file format ( http://genome.ucsc.

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Data format error: expecting at least 3 fields in BED file

use of liftOver with a PLINK BED file. A PLINK BED file is not the same thing as a UCSC BED (Browser Extensible Data) file. You can review the UCSC BED file format ( http://genome.ucsc.

10/15/25

Doan Thao Dinh, … Gerardo Perez6

10/3/25

liftover between assemblies query

The reciprocal liftOver chain files (GCF_028372415.1 to mm10 / GCF_028372415.1 to hg38) are available on our download server: GCF_028372415.1 to mm10: https://hgdownload.soe

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liftover between assemblies query

The reciprocal liftOver chain files (GCF_028372415.1 to mm10 / GCF_028372415.1 to hg38) are available on our download server: GCF_028372415.1 to mm10: https://hgdownload.soe

10/3/25

Lawson, Nathan, Matthew Speir3

9/26/25

GRCz12 liftover

for your LiftOver file request. These files are now available on our download server: * https://hgdownload.gi.ucsc.edu/hubs/GCF/049/306/965/GCF_049306965.1/liftOver/GCF_049306965

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GRCz12 liftover

for your LiftOver file request. These files are now available on our download server: * https://hgdownload.gi.ucsc.edu/hubs/GCF/049/306/965/GCF_049306965.1/liftOver/GCF_049306965

9/26/25

Mireia Marín Ginestar, Jairo Navarro Gonzalez2

9/25/25

Why to not liftover SNPS

why the Liftover Tool should, specifically, not be > used for SNPs. Do you expect SNPs uncorrectly lifted or a higher drop out > ratio? > Thanks for your attention and sorry

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Why to not liftover SNPS

why the Liftover Tool should, specifically, not be > used for SNPs. Do you expect SNPs uncorrectly lifted or a higher drop out > ratio? > Thanks for your attention and sorry

9/25/25

lixinmei, Matthew Speir2

9/22/25

Request help regarding the chain file

for your LiftOver file request. These files are now on our download server: - https://hgdownload.soe.ucsc.edu/hubs/GCF/048/773/025/GCF_048773025.1/liftOver/GCF_048773025

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Request help regarding the chain file

for your LiftOver file request. These files are now on our download server: - https://hgdownload.soe.ucsc.edu/hubs/GCF/048/773/025/GCF_048773025.1/liftOver/GCF_048773025

9/22/25

周亚琦, Luis Nassar2

9/15/25

USCS LiftOver Queries

The requested liftOver file can now be found on our download server: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToGCF_009873245.2.over.chain.gz On

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USCS LiftOver Queries

The requested liftOver file can now be found on our download server: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToGCF_009873245.2.over.chain.gz On

9/15/25

Yixuan Xin, Luis Nassar2

9/2/25

Liftover RN7 to RN8 Doesn't Working

rn5/liftOver/rn5ToGCF_036323735.1.over.chain.gz We're not familiar with how you are importing it to R (rttracklayer?), but if the rn8 assembly has UCSC-style chromosome

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Liftover RN7 to RN8 Doesn't Working

rn5/liftOver/rn5ToGCF_036323735.1.over.chain.gz We're not familiar with how you are importing it to R (rttracklayer?), but if the rn8 assembly has UCSC-style chromosome

9/2/25

Yang, Jingjing, Jairo Navarro Gonzalez3

8/15/25

Help solve the issue of running the tool in our HPC system

running the LiftOver standalone tool in our HPC system. I have the following errors, and it won't be possible for us to get higher version of the GLBC in our current system. I am wondering

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Help solve the issue of running the tool in our HPC system

running the LiftOver standalone tool in our HPC system. I have the following errors, and it won't be possible for us to get higher version of the GLBC in our current system. I am wondering

8/15/25

Meng, Fan, Hiram Clawson2

8/14/25

Rn8 to Rn7 liftover

, the liftOver files are available at: https://hgdownload.soe.ucsc.edu/hubs/GCF/036/323/735/GCF_036323735.1/liftOver/GCF_036323735.1ToRn7.over.chain.gz and https

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Rn8 to Rn7 liftover

, the liftOver files are available at: https://hgdownload.soe.ucsc.edu/hubs/GCF/036/323/735/GCF_036323735.1/liftOver/GCF_036323735.1ToRn7.over.chain.gz and https

8/14/25

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