Re: [genome] Post the question to the forum
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Cath Tyner
Mar 23, 2017, 11:44:55 AM3/23/17
to 范凯俐, UCSC Genome Browser Public Help Forum
Hello Kaili,
Thank you for your follow-up question to the UCSC Genome Browser support forum. You are correct, by simply emailing us at gen...@soe.ucsc.edu, you have successfully posted to the support forum.
The file calJac3ToRn6.over.chain.gz was mistakingly included on the list of available files; but we do not have this file. My apologies for the inconvenience - the spreadsheet has been updated to reflect that we do not have this file.
Please respond to this list if you have further questions!
* Unsubscribe: Email genome-announce+unsubscribe@soe.ucsc.edu
Thank you again for your inquiry and for using the UCSC Genome Browser.
Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:
* Confidential/private help: Email
genom...@soe.ucsc.eduUCSC Genome Browser Announcements List (email alerts for new data & software):
* Subscribe: Email genome-announce+subscribe@soe.ucsc.edu * Unsubscribe: Email genome-announce+unsubscribe@soe.ucsc.edu
On Wed, Mar 22, 2017 at 9:12 PM, 范凯俐 <fankai...@gmail.com> wrote:
Hello,--Actually I don’t quite sure how to post my question. After I email you ,anything else?Thanks!Best,KailiBegin forwarded message:From: Cath Tyner <ca...@ucsc.edu>Subject: Re: [genome] For more pairwise alignment dataDate: 22 March 2017 at 9:45:27 PM GMT+8To: 范凯俐 <fankai...@gmail.com>Hello Kaili,This is a great question! To move forward, please note that the UCSC Genome Browser support team requires that all new and follow-up questions be posted to one of our support forums. In order to best assist you, could you please post your question to one of the forums listed below?The benefit of posting the question is that our entire support team, including engineers with various expertise, will see your question and we will be able to provide the best support to you. I look forward to helping you further once your question is posted! * Confidential/private help: Emailgenom...@soe.ucsc.eduUCSC Genome Browser Announcements List (email alerts for new data & software):* Subscribe: Email genome-announce+subscribe...@soe.ucsc.edu
* Unsubscribe: Email genome-announce+unsubscri...@soe.ucsc.eduOn Mar 22, 2017 12:36 AM, "范凯俐" <fankai...@gmail.com> wrote:Hello Cath,I found there is something wrong in the file calJac3ToRn6.over.chain.gz in the sheet you gave me, where the download address is brokeDo you have another link for this?Thanks!Best,KailiOn 28 Feb 2017, at 9:25 AM, Cath Tyner <ca...@ucsc.edu> wrote:Hello Kaili,
Thank you for putting together a list of requested files, that was very helpful in assessing your request. Of the 55 files that you requested, we do have 15 of those files on our development server, as listed in thisspreadsheet.
Unfortunately, it would require a lot of time to generate the other 40 files, and due to limited resources, we don't have the ability to accomplish your request at this time. However, I can recommend some resources where you can look into the possibility of creating these files yourself:
Resources:
UCSC Genome Browser wiki page
UCSC Genome Browser support forum
Here, you can search for related search terms, such as:
"http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto"
For example, see
You can search for other terms, such as "whole genome alignment", "aligning sequences", "pairwise alignment" etc.
From the "Whole_genome_alignment_howto" wiki page, specifically take note of the script: http://genomewiki.ucsc.edu/images/9/93/RunLastzChain_sh.txt
Note that you can also use "RunLastzChain_sh.txt" as a search term in thesupport forum.
You may also find other resources on sites like www.biostars.org, searching for "Whole_genome_alignment_howto".
For example: https://www.biostars.org/p/11263/
If you do move forward with creating the other files you require, please know that you can continue to ask questions on this mailing list if you cannot find answers in the support forum.Please respond to this list if you have further questions!Thank you again for your inquiry and for using the UCSC Genome Browser.Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below: * Confidential/private help: Emailgenom...@soe.ucsc.eduUCSC Genome Browser Announcements List (email alerts for new data & software):* Subscribe: Email genome-announce+subscribe...@soe.ucsc.edu
* Unsubscribe: Email genome-announce+unsubscri...@soe.ucsc.eduOn Wed, Feb 22, 2017 at 10:10 PM, 范凯俐 <fankai...@gmail.com> wrote:Dear Sir or Madam,I am a bioinformatics Master student in China.Now I am working on a piRNA evolution project in several species. I want to know some syntenic regions in different species.I have looked over all the chain files in UCSC database(for the mm10ToHg38.over.chain.gz and this like files), but it doesn’t cover all I need. Could you please give me some help about these data?<Screen Shot 2017-02-23 at 11.18.09 AM.png>I made a table shows in above.I work on ten species, and the red ones are those data I can find in your database.(e.g.: there is hg38ToMonDom5.over.chain.gz, but no monDom5ToHg38.over.chain.gz file)Thus, all the while blank are the data I need. I know there are a lot, but it would be really great if you could help.Thank you very much!Best,
KaliKaili FanDepartment of Bioinformatics
School of Life Science and Technology
Tongji University
Room 1012, Medicine Building
NO.1239 Siping Road
Shanghai, 200092, P.R.China--
---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser discussion list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
Begin forwarded message:From: Cath Tyner <ca...@ucsc.edu>Subject: Re: [genome] For more pairwise alignment dataDate: 28 February 2017 at 9:25:06 AM GMT+8To: 范凯俐 <fankai...@gmail.com>Cc: UCSC Genome Browser Public Help Forum <gen...@soe.ucsc.edu>Hello Kaili,
Thank you for putting together a list of requested files, that was very helpful in assessing your request. Of the 55 files that you requested, we do have 15 of those files on our development server, as listed in thisspreadsheet.
Unfortunately, it would require a lot of time to generate the other 40 files, and due to limited resources, we don't have the ability to accomplish your request at this time. However, I can recommend some resources where you can look into the possibility of creating these files yourself:
Resources:
UCSC Genome Browser wiki page
UCSC Genome Browser support forum
Here, you can search for related search terms, such as:
"http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto"
For example, see
You can search for other terms, such as "whole genome alignment", "aligning sequences", "pairwise alignment" etc.
From the "Whole_genome_alignment_howto" wiki page, specifically take note of the script: http://genomewiki.ucsc.edu/images/9/93/RunLastzChain_sh.txt
Note that you can also use "RunLastzChain_sh.txt" as a search term in thesupport forum.
You may also find other resources on sites like www.biostars.org, searching for "Whole_genome_alignment_howto".
For example: https://www.biostars.org/p/11263/
If you do move forward with creating the other files you require, please know that you can continue to ask questions on this mailing list if you cannot find answers in the support forum.Please respond to this list if you have further questions!Thank you again for your inquiry and for using the UCSC Genome Browser.Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below: * Confidential/private help: Emailgenom...@soe.ucsc.eduUCSC Genome Browser Announcements List (email alerts for new data & software):* Subscribe: Email genome-announce+subs...@soe.ucsc.edu
* Unsubscribe: Email genome-announce+unsub...@soe.ucsc.eduOn Wed, Feb 22, 2017 at 10:10 PM, 范凯俐 <fankai...@gmail.com> wrote:Dear Sir or Madam,I am a bioinformatics Master student in China.Now I am working on a piRNA evolution project in several species. I want to know some syntenic regions in different species.I have looked over all the chain files in UCSC database(for the mm10ToHg38.over.chain.gz and this like files), but it doesn’t cover all I need. Could you please give me some help about these data?I made a table shows in above.I work on ten species, and the red ones are those data I can find in your database.(e.g.: there is hg38ToMonDom5.over.chain.gz, but no monDom5ToHg38.over.chain.gz file)Thus, all the while blank are the data I need. I know there are a lot, but it would be really great if you could help.Thank you very much!Best,
KaliKaili FanDepartment of Bioinformatics
School of Life Science and Technology
Tongji University
Room 1012, Medicine Building
NO.1239 Siping Road
Shanghai, 200092, P.R.China--
---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser discussion list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
Begin forwarded message:From: Cath Tyner <ca...@ucsc.edu>Subject: Re: [genome] For more pairwise alignment dataDate: 24 February 2017 at 10:48:17 AM GMT+8To: 范凯俐 <fankai...@gmail.com>Cc: UCSC Genome Browser Public Help Forum <gen...@soe.ucsc.edu>Hello Kali,Thank you for using the UCSC Genome Browser and for inquiring about the generation of liftOver files. In order to best assist you, could you please respond to this mailing list and provide a list of exactly which files you need (instead of the chart/table)? Please list EVERY file that you would like to have, and then our support team can assess the requested list to see if it is possible to generate the files. * Confidential/private help: Emailgenom...@soe.ucsc.eduUCSC Genome Browser Announcements List (email alerts for new data & software):* Subscribe: Email genome-announce+subs...@soe.ucsc.edu
* Unsubscribe: Email genome-announce+unsub...@soe.ucsc.eduOn Wed, Feb 22, 2017 at 10:10 PM, 范凯俐 <fankai...@gmail.com> wrote:Dear Sir or Madam,I am a bioinformatics Master student in China.Now I am working on a piRNA evolution project in several species. I want to know some syntenic regions in different species.I have looked over all the chain files in UCSC database(for the mm10ToHg38.over.chain.gz and this like files), but it doesn’t cover all I need. Could you please give me some help about these data?I made a table shows in above.I work on ten species, and the red ones are those data I can find in your database.(e.g.: there is hg38ToMonDom5.over.chain.gz, but no monDom5ToHg38.over.chain.gz file)Thus, all the while blank are the data I need. I know there are a lot, but it would be really great if you could help.Thank you very much!Best,
KaliKaili FanDepartment of Bioinformatics
School of Life Science and Technology
Tongji University
Room 1012, Medicine Building
NO.1239 Siping Road
Shanghai, 200092, P.R.China--
---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser discussion list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
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You received this message because you are subscribed to the Google Groups "UCSC Genome Browser discussion list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
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