User: ablanchetcohen
ablanchetcohen • 1.2k
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Posts by ablanchetcohen
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Comment:
C: how I can put tophat in path?
... Normally, unzipping the file should suffice.
You might want to add tophat to your PATH, and you might want to verify that Python2 is installed, which should be the case. ...
written 2.6 years ago by
ablanchetcohen • 1.2k
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Comment:
C: how I can put tophat in path?
... It makes no difference.
Just use the name of the program to call it:
tophat
-p is an argument to the program.
There should always be a space between the call to the program, and the arguments to the program.
...
written 2.6 years ago by
ablanchetcohen • 1.2k
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... **Summary of responsibilities**
The successful candidate will work in the collection, management, interpretation, and analysis of biological/clinical data, with a focus on deep or next-generation sequencing data. His/Her time will be devoted to IRCM’s Bioinformatics Core Facility (BIF). BIF handles ...
written 2.7 years ago by
ablanchetcohen • 1.2k
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... Right. Sorry. I meant NCBI. ...
written 2.7 years ago by
ablanchetcohen • 1.2k
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... Same here.
Good old wget works better than all the other solutions proposed by EBI. ...
written 2.7 years ago by
ablanchetcohen • 1.2k
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... I have written my own, but they're not quite ready for release.
The MUGQIC have released their pipelines on Bitbucket, but they're quite complicated to use.
If you really do a lot of analyses, you'll end up finding that the best option is just to write your own scripts.
If you only do a few analyse ...
written 2.8 years ago by
ablanchetcohen • 1.2k
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... 1. STAR is currently the most widely-used aligner for RNA-Seq data. It
is extremely fast, but memory hungry. STAR is the aligner I
currently use, after having used TopHat for several years.
TopHat still works fine, but has unfortunately been declared
obsolete by its developers ...
written 2.8 years ago by
ablanchetcohen • 1.2k
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Comment:
C: Pathway Analysis papers anyone?
... GSEA does integrate the fold-changes and the p-values, but it is more of an enrichment analysis then an actual pathway analysis like IPA.
You don't get an actual pathway from GSEA. ...
written 2.8 years ago by
ablanchetcohen • 1.2k
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Comment:
C: Pathway Analysis papers anyone?
... Why do none of these open source programs attempt to do like IPA and integrate the fold changes or the p-values into the pathway analysis? ...
written 2.8 years ago by
ablanchetcohen • 1.2k
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... This is the first paper that a quick Google search returned.
Pathway-based Analysis Tools for Complex Diseases: A Review
http://www.sciencedirect.com/science/article/pii/S1672022914001065
It's just a description of the pathway analysis tools available though.
I'm interested in the subject since I ...
written 2.8 years ago by
ablanchetcohen • 1.2k
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