User: ablanchetcohen

gravatar for ablanchetcohen
ablanchetcohen1.2k
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Canada
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3 years, 1 month ago
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Posts by ablanchetcohen

<prev • 91 results • page 1 of 10 • next >
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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 3.1 years ago by ablanchetcohen1.2k
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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 3.1 years ago by ablanchetcohen1.2k
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Job: Bioinformatics analyst at IRCM, in Montreal, Canada
... **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 ...
job bioinformatics analyst written 3.2 years ago by ablanchetcohen1.2k
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Comment: C: fastq-dump error: transfer unknown
... Right. Sorry. I meant NCBI. ...
written 3.2 years ago by ablanchetcohen1.2k
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Comment: C: fastq-dump error: transfer unknown
... Same here. Good old wget works better than all the other solutions proposed by EBI. ...
written 3.2 years ago by ablanchetcohen1.2k
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Comment: C: How to map RNA-seq reads of a species to a reference genome of another close spe
... 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 3.2 years ago by ablanchetcohen1.2k
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Answer: A: How to map RNA-seq reads of a species to a reference genome of another close spe
... 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 3.2 years ago by ablanchetcohen1.2k
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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 3.3 years ago by ablanchetcohen1.2k
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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 3.3 years ago by ablanchetcohen1.2k
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Answer: A: Pathway Analysis papers anyone?
... 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 3.3 years ago by ablanchetcohen1.2k

Latest awards to ablanchetcohen

Guru 3.3 years ago, received more than 100 upvotes.
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: what is the biological replications
Scholar 3.3 years ago, created an answer that has been accepted. For A: IGV not reading BAM file
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Scholar 3.3 years ago, created an answer that has been accepted. For A: htseq-count produces no features amid alignment
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