Groups
Sign in
Groups
UCSC Genome Browser Public Support
Conversations
Labels
About
Send feedback
Help
Sort By Relevance
Sort By Date
1–30 of many
Gordon, Martin
May 30
GCF_030867095.1 chain file generation & question on workflow
title=
DoBlastzChainNet
.
pl
I have found a nextflow pipeline available that simplifies the process that I am using myself to generate these files. https://nf-lo.readthedocs.io
unread,
GCF_030867095.1 chain file generation & question on workflow
title=
DoBlastzChainNet
.
pl
I have found a nextflow pipeline available that simplifies the process that I am using myself to generate these files. https://nf-lo.readthedocs.io
May 30
Meyer, Rick - REE-ARS
,
Jairo Navarro Gonzalez
2
Jan 26
LiftOver Chain Files for Soy Genome Conversions
using the
DoBlastzChainNet
.
pl
script that can be found on the following wiki page: https://genomewiki.ucsc.edu/index.php/
DoBlastzChainNet
.
pl
You can see an example of the script
unread,
LiftOver Chain Files for Soy Genome Conversions
using the
DoBlastzChainNet
.
pl
script that can be found on the following wiki page: https://genomewiki.ucsc.edu/index.php/
DoBlastzChainNet
.
pl
You can see an example of the script
Jan 26
Giulio Genovese
, …
Jairo Navarro Gonzalez
9
12/29/23
hg19ToHg38.over.chain.gz
DoSameSpeciesLiftOver.
pl
from BLAT alignments > 2) hg38ToHs1.over.chain.gz was generated by UCSC using
DoBlastzChainNet
.
pl
> from LASTZ alignments > 3) hg38-chm13v2
unread,
hg19ToHg38.over.chain.gz
DoSameSpeciesLiftOver.
pl
from BLAT alignments > 2) hg38ToHs1.over.chain.gz was generated by UCSC using
DoBlastzChainNet
.
pl
> from LASTZ alignments > 3) hg38-chm13v2
12/29/23
Dongwu Zhan
,
Gerardo Perez
2
11/22/23
Question about liftOver chain file (between species)
have the
doBlastzChainNet
.
pl
script/process which was used to create the hg19 to mm9 liftOver chain file: https://genomewiki.ucsc.edu/index.php/
DoBlastzChainNet
.
pl
. The
unread,
Question about liftOver chain file (between species)
have the
doBlastzChainNet
.
pl
script/process which was used to create the hg19 to mm9 liftOver chain file: https://genomewiki.ucsc.edu/index.php/
DoBlastzChainNet
.
pl
. The
11/22/23
刘子玮
, …
Luis Nassar
3
10/31/23
Bug happened when running UCSC-doBlastzChainNet.pl pipeline
php/
DoBlastzChainNet
.
pl
#The_new_streamline_pairLastz_script >> at the step of running
DoBlastzChainNet
.
pl
. ( I used localhost instead of >> other host names
unread,
Bug happened when running UCSC-doBlastzChainNet.pl pipeline
php/
DoBlastzChainNet
.
pl
#The_new_streamline_pairLastz_script >> at the step of running
DoBlastzChainNet
.
pl
. ( I used localhost instead of >> other host names
10/31/23
Demayo, James
, …
Matthew Speir
18
9/13/23
Adding chain files for new assemblies
php/
DoBlastzChainNet
.
pl
#lastz_parameter_file http://genomewiki.ucsc.edu/index.php/Lastz_DEF_file_parameters You can also review the following makedocs for some example
unread,
Adding chain files for new assemblies
php/
DoBlastzChainNet
.
pl
#lastz_parameter_file http://genomewiki.ucsc.edu/index.php/Lastz_DEF_file_parameters You can also review the following makedocs for some example
9/13/23
肖稳
,
Gerardo Perez
2
3/17/23
new genome
used the
doBlastzChainNet
.
pl
script with the lastz parameters since it tends to do better for human-rodent distances or greater. We offer some example lastz parameters on the following
unread,
new genome
used the
doBlastzChainNet
.
pl
script with the lastz parameters since it tends to do better for human-rodent distances or greater. We offer some example lastz parameters on the following
3/17/23
Fabien Sassolas
,
Jairo Navarro Gonzalez
2
11/10/22
Chain files for mm10 vs other mice genome
myself using
doBlastzChainNet
.
pl
> but that doesn't seems to be the recommended way. > > Thanks in advance, > Regards, > Fabien Sassolas, PhD student @IGFL >
unread,
Chain files for mm10 vs other mice genome
myself using
doBlastzChainNet
.
pl
> but that doesn't seems to be the recommended way. > > Thanks in advance, > Regards, > Fabien Sassolas, PhD student @IGFL >
11/10/22
William Thomas
,
Jairo Navarro Gonzalez
2
11/30/21
path issue doBlastzChainNet.pl
partitionSequence.
pl
32100000 10000 /gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/dm6.2bit /gpfs/scratch/withomas/project_noRoot_MGA/data/genomes
unread,
path issue doBlastzChainNet.pl
partitionSequence.
pl
32100000 10000 /gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/dm6.2bit /gpfs/scratch/withomas/project_noRoot_MGA/data/genomes
11/30/21
B. Osberg
,
Hiram Clawson
2
10/22/21
LiftOver chain file generation for nothobranchius furzeri
php/
DoBlastzChainNet
.
pl
> > It seems that some of the software at that latter link is specific to the architecture on your > system, however. For example, the [Parasol Job
unread,
LiftOver chain file generation for nothobranchius furzeri
php/
DoBlastzChainNet
.
pl
> > It seems that some of the software at that latter link is specific to the architecture on your > system, however. For example, the [Parasol Job
10/22/21
王睿
,
Brian Lee
2
8/26/21
blastz
mention of
doBlastzChainNet
.
pl
that would be useful to review: https://groups.google.com/a/soe.ucsc.edu/g/genome/search?q=
doBlastzChainNet
.
pl
Thank you again for your
unread,
blastz
mention of
doBlastzChainNet
.
pl
that would be useful to review: https://groups.google.com/a/soe.ucsc.edu/g/genome/search?q=
doBlastzChainNet
.
pl
Thank you again for your
8/26/21
Fu weiwei
,
Hiram Clawson
2
9/4/20
pipeline for whole genome alignment used in UCSC genome browser
php/
DoBlastzChainNet
.
pl
This describes the process of using our scripting tool chain that performs a whole genome alignment. You can view the actual script in our source tree: https
unread,
pipeline for whole genome alignment used in UCSC genome browser
php/
DoBlastzChainNet
.
pl
This describes the process of using our scripting tool chain that performs a whole genome alignment. You can view the actual script in our source tree: https
9/4/20
TALENTI Andrea
,
Hiram Clawson
4
5/13/20
Question regarding different species liftover
at the
doBlastzChainNet
.
pl
, it looks like you proceed in the following way: > > 1. Align with blastz with proper parameters and save as lav > 2. Convert to psl with lavToAxt
unread,
Question regarding different species liftover
at the
doBlastzChainNet
.
pl
, it looks like you proceed in the following way: > > 1. Align with blastz with proper parameters and save as lav > 2. Convert to psl with lavToAxt
5/13/20
Saroja Somasundaram
, …
Luis Nassar
4
3/24/20
liftOver from scaffold to genome assembly
php/
DoBlastzChainNet
.
pl
): - *
DoBlastzChainNet
.
pl
* - which is focused on creating chains between two assemblies from different organisms (eg mouse mm10 and human hg38) - This answer
unread,
liftOver from scaffold to genome assembly
php/
DoBlastzChainNet
.
pl
): - *
DoBlastzChainNet
.
pl
* - which is focused on creating chains between two assemblies from different organisms (eg mouse mm10 and human hg38) - This answer
3/24/20
zo...@sustech.edu.cn
,
Brian Lee
2
2/4/20
Could you help me build liftover chains for Mus_Caroli to mm10 and Mus_Pahari to mm10
: -
DoBlastzChainNet
.
pl
- which is focused on creating chains between two assemblies from different organisms (eg mouse mm10 and human hg38) - If this is what you're after, then
unread,
Could you help me build liftover chains for Mus_Caroli to mm10 and Mus_Pahari to mm10
: -
DoBlastzChainNet
.
pl
- which is focused on creating chains between two assemblies from different organisms (eg mouse mm10 and human hg38) - If this is what you're after, then
2/4/20
Ciro Ramirez Suastegui
,
Matthew Speir
2
1/24/20
Chain file creation
: -
DoBlastzChainNet
.
pl
- which is focused on creating chains between two assemblies from different organisms (eg mouse mm10 and human hg38) - If this is what you're after, then
unread,
Chain file creation
: -
DoBlastzChainNet
.
pl
- which is focused on creating chains between two assemblies from different organisms (eg mouse mm10 and human hg38) - If this is what you're after, then
1/24/20
Aimei Dai
, …
Hiram Clawson
6
11/26/19
Whole genome alignment of dm6 to droSim1
constructLiftFile.
pl
is different to other fragments. I changed the constructLiftFile.
pl
and solved this problem, but other chromosomes (such as chr4) arised the same problem
unread,
Whole genome alignment of dm6 to droSim1
constructLiftFile.
pl
is different to other fragments. I changed the constructLiftFile.
pl
and solved this problem, but other chromosomes (such as chr4) arised the same problem
11/26/19
李梓锋Lee_ZiFung
,
Jairo Navarro Gonzalez
2
11/6/19
Some Question About Lastz And Alignment
. The
doBlastzChainNet
.
pl
script will create a pairwise alignment and the lastz parameters are defined inside a DEF file. Some example lastz parameters used for human can be found
unread,
Some Question About Lastz And Alignment
. The
doBlastzChainNet
.
pl
script will create a pairwise alignment and the lastz parameters are defined inside a DEF file. Some example lastz parameters used for human can be found
11/6/19
李梓锋Lee_ZiFung
,
Daniel Schmelter
2
10/18/19
Blind Mole Rat
doBlatzChainsNets.
pl
, which requires 2bit and chrom.sizes input files. Generating these will require two additional utilities "faToTwoBit" and "faSizes -detailed
unread,
Blind Mole Rat
doBlatzChainsNets.
pl
, which requires 2bit and chrom.sizes input files. Generating these will require two additional utilities "faToTwoBit" and "faSizes -detailed
10/18/19
Matt, Gavriel
,
Daniel Schmelter
2
10/4/19
canFam3 phastCons scores
php/
DoBlastzChainNet
.
pl
Once you have your pairwise MAF files made, you will need to run the MultiZ program to generate multi-species MAF files. For a reference on how a 5-way MultiZ
unread,
canFam3 phastCons scores
php/
DoBlastzChainNet
.
pl
Once you have your pairwise MAF files made, you will need to run the MultiZ program to generate multi-species MAF files. For a reference on how a 5-way MultiZ
10/4/19
Dominik Hadžega
,
Daniel Schmelter
2
9/11/19
chain alignment track of multiple genomes
with the
doBlastzChainNet
.
pl
script, producing pairwise MAF files 2. Collect those pairwise-MAF files in one place, run MultiZ to produce a multi-species MAF file 3. Visualize that
unread,
chain alignment track of multiple genomes
with the
doBlastzChainNet
.
pl
script, producing pairwise MAF files 2. Collect those pairwise-MAF files in one place, run MultiZ to produce a multi-species MAF file 3. Visualize that
9/11/19
ding dominique
,
Luis Nassar
2
3/26/19
Request for unpublished genome assembly chain files
DoSameSpeciesLiftOver.
pl
) and a second for more general liftOver chains ( http://genomewiki.ucsc.edu/index.php/
DoBlastzChainNet
.
pl
). If you have issues throughout the process
unread,
Request for unpublished genome assembly chain files
DoSameSpeciesLiftOver.
pl
) and a second for more general liftOver chains ( http://genomewiki.ucsc.edu/index.php/
DoBlastzChainNet
.
pl
). If you have issues throughout the process
3/26/19
Irene Miriam Kaplow
,
Jairo Navarro Gonzalez
2
3/5/19
(B)LASTZ Parameters for Creating Liftover Chains for Mapping between Different Assemblies of the Same Species
DoSameSpeciesLiftOver.
pl
Unfortunately, it is beyond the scope of this mailing list to provide scientific advice such as the lastz parameters to use to generate your alignments
unread,
(B)LASTZ Parameters for Creating Liftover Chains for Mapping between Different Assemblies of the Same Species
DoSameSpeciesLiftOver.
pl
Unfortunately, it is beyond the scope of this mailing list to provide scientific advice such as the lastz parameters to use to generate your alignments
3/5/19
Shuai Dominique Ding
,
Christopher Lee
2
9/13/18
Request for Dsim2 to Dm6 chain file
php/
DoBlastzChainNet
.
pl
Please let us know if you have any further questions! Thanks, Christopher Lee UCSC Genomics Institute On Wed, Sep 12, 2018 at 3:44 AM, Shuai Dominique Ding
unread,
Request for Dsim2 to Dm6 chain file
php/
DoBlastzChainNet
.
pl
Please let us know if you have any further questions! Thanks, Christopher Lee UCSC Genomics Institute On Wed, Sep 12, 2018 at 3:44 AM, Shuai Dominique Ding
9/13/18
Pritesh Sabara
,
Jairo Navarro Gonzalez
2
9/6/18
Regarding PhestCons and phyloCSF
php/
DoBlastzChainNet
.
pl
Our makeDb/doc/* files have many examples of how to run multiz and phastCons on a few species. For example, bosTau4.txt shows the steps that one of our engineers
unread,
Regarding PhestCons and phyloCSF
php/
DoBlastzChainNet
.
pl
Our makeDb/doc/* files have many examples of how to run multiz and phastCons on a few species. For example, bosTau4.txt shows the steps that one of our engineers
9/6/18
Kritika Karri
,
Christopher Lee
2
8/2/18
rn6ToMm9.over.chain.gz
php/
DoBlastzChainNet
.
pl
Please let us know if you have any further questions! Thanks, Christopher Lee UCSC Genomics Institute Want to share the Browser with colleagues? Host a workshop
unread,
rn6ToMm9.over.chain.gz
php/
DoBlastzChainNet
.
pl
Please let us know if you have any further questions! Thanks, Christopher Lee UCSC Genomics Institute Want to share the Browser with colleagues? Host a workshop
8/2/18
Liming Li
,
Christopher Lee
2
5/3/18
Request for hg19TopanPan2.fa.over.chain.gz and hg19TogorGor5.fa.over.chain.gz
php/
DoBlastzChainNet
.
pl
Please let us know if you have any further questions! Thanks, Christopher Lee UCSC Genomics Institute Want to share the Browser with colleagues? Host a workshop
unread,
Request for hg19TopanPan2.fa.over.chain.gz and hg19TogorGor5.fa.over.chain.gz
php/
DoBlastzChainNet
.
pl
Please let us know if you have any further questions! Thanks, Christopher Lee UCSC Genomics Institute Want to share the Browser with colleagues? Host a workshop
5/3/18
Batra, Sajeev
,
Hiram Clawson
3
4/26/18
Creating an ooc file for chain file generation
doSameSpeciesLiftOver.
pl
script from the UCSC github: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/hg/utils/automation/doSameSpeciesLiftOver
unread,
Creating an ooc file for chain file generation
doSameSpeciesLiftOver.
pl
script from the UCSC github: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/hg/utils/automation/doSameSpeciesLiftOver
4/26/18
Feng Tian
, …
Luvina Guruvadoo
4
2/27/17
About the process of genome alignment
UCSC)
doBlastzChainNet
.
pl
: >> http://genomewiki.ucsc.edu/index.php/Blastz >> >> It is said the repeat sequences were removed before alignment: >>
unread,
About the process of genome alignment
UCSC)
doBlastzChainNet
.
pl
: >> http://genomewiki.ucsc.edu/index.php/Blastz >> >> It is said the repeat sequences were removed before alignment: >>
2/27/17
Arumilli, Meharji
9/13/16
Dog-Bear Sequence Alignment
Whole_genome_alignment_howto#
doBlastzChainNet
.
pl
" replacing blastz with lastz. Species1 directory: "Dog" which has 38 chromosomes in the directory Species2
unread,
Dog-Bear Sequence Alignment
Whole_genome_alignment_howto#
doBlastzChainNet
.
pl
" replacing blastz with lastz. Species1 directory: "Dog" which has 38 chromosomes in the directory Species2
9/13/16