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shenlab-sinai / region_analysis

A python script used to annotate genomic intervals.
GNU General Public License v3.0
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sacCer3 genome for diffReps #30

Open mayre opened 9 years ago

mayre commented 9 years ago

Hello,

I would like to try out diffReps on some ChIP-seq data that I have recently analyzed by MACS2. Could you please add the relevant genome files for this? sacCer3 is the most updated one.

Thank you! Mayuri

lishen commented 9 years ago

Ningyi, have you added this genome already?

Li

On Tue, Feb 17, 2015 at 6:52 PM, mayre notifications@github.com wrote:

Hello,

I would like to try out diffReps on some ChIP-seq data that I have recently analyzed by MACS2. Could you please add the relevant genome files for this? sacCer3 is the most updated one.

Thank you! Mayuri

— Reply to this email directly or view it on GitHub https://github.com/shenlab-sinai/region_analysis/issues/30.

Li Shen, Ph.D. Computer Science Assistant Professor Department of Neuroscience Icahn School of Medicine at Mount Sinai New York, NY 10029 ################# ngs.plot - the coolest NGS plotting tool: https://code.google.com/p/ngsplot/ Want ChIP-seq differential analysis? Use: https://code.google.com/p/diffreps/

ny-shao commented 9 years ago

No, sacCer3 is not added. sacCer3 is not included in UCSC Refseq database, so I could not add it in region_analysis.

mayre commented 9 years ago

Hello Ning-Yi,

You are correct that there is no Refseq database, however, according to the following question on the UCSC Genome Browser forum, the dump can be downloaded from this (modified) link:

Original question: http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=17612&S=8d77afde194cc68e9d4069d483ae8828

Recommendation: http://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/database/

The links from the forum seem to be broken?...

Please let me know if these files will work. Thank you!

Best, Mayuri