sacCer3 genome for diffReps
Opened this issue · 3 comments
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
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/
No, sacCer3 is not added. sacCer3 is not included in UCSC Refseq database, so I could not add it in region_analysis.
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