sacCer3 genome for diffReps

[mayre]

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]

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
#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]

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

[mayre]

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