Reg: liftover chain file to convert hg18 to hg19

[Mayur Divate]

Dear Sir/Madam,

can you please provide me liftover dependency (hg18Tohg19) chain file?

Thanks and Regards,

Mayur

Mayur Divate
Research Assistant (Bioinformatics)

Faculty of Health Sciences,

University of Macau,
Avenida da Universidade,

Taipa, Macau, SAR China

Mobile: +91 80 87 127314  or + 853 6299 1370

      
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[Brian Lee]

Dear Mayur,

Thank you for using the UCSC Genome Browser and your question about obtaining the liftOver (hg18Tohg19) chain file.

From our main page, http://genome.ucsc.edu/index.html, on the left hand side you will find a link titled "Downloads".

If you click that link you will arrive to our Download server: http://hgdownload.soe.ucsc.edu/downloads.html

On the Downloads page, you can click the "Human" link and then scroll down to the "Mar. 2006 (hg18)" section and find a "LiftOver files" section: http://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/

Please see the top displayed message on the liftOver page and there you can also find the hg18ToHg19.over.chain.gz file.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply toge...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genome Bioinformatics Group

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[Mayur Divate]

Dear Brain Lee,

I found the solution and able to complete.

Regards,

Mayur

Mayur Divate
Research Assistant (Bioinformatics)

Faculty of Health Sciences,

University of Macau,
Avenida da Universidade,

Taipa, Macau, SAR China

Mobile: +91 80 87 127314  or + 853 6299 1370

      
Confidentiality Note: If you received this email in error please delete and notify sender.

On 29 September 2015 at 11:44, Mayur Divate <mdi...@umac.mo> wrote:

Dear Brian Lee,

I cant find parameter to mention chain file, can you please help me to build command for running liftover.

I would like to default parameters.

I am using errorHelp parameter to debug, but it not much helpful for me.

I have alignment data in bed file format. {chr start end name }

Regards,

Mayur

Mayur Divate
Research Assistant (Bioinformatics)

Faculty of Health Sciences,

University of Macau,
Avenida da Universidade,

Taipa, Macau, SAR China

Mobile: +91 80 87 127314  or + 853 6299 1370

      
Confidentiality Note: If you received this email in error please delete and notify sender.

[Mayur Divate]

Dear Brian Lee,

I cant find parameter to mention chain file, can you please help me to build command for running liftover.

I would like to default parameters.

I am using errorHelp parameter to debug, but it not much helpful for me.

I have alignment data in bed file format. {chr start end name }

Regards,

Mayur

Mayur Divate
Research Assistant (Bioinformatics)

Faculty of Health Sciences,

University of Macau,
Avenida da Universidade,

Taipa, Macau, SAR China

Mobile: +91 80 87 127314  or + 853 6299 1370

      
Confidentiality Note: If you received this email in error please delete and notify sender.

On 26 September 2015 at 04:15, Brian Lee <bria...@soe.ucsc.edu> wrote: