User: Paolo Guarnieri

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United States
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4 years, 8 months ago
Joined:
7 years, 4 months ago
Email:
p*****@columbia.edu

Posts by Paolo Guarnieri

<prev • 6 results • page 1 of 1 • next >
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Answer: A: SGSeq error on analyzeFeatures
... Just got the alignments from STAR (STAR_2.4.0h1) and it works just fine, with no errors. the parameter you refer to is "--outSAMstrandField intronMotif", which enables that tag. Now the function "getBamInfo" Recognizes fragment size and that is paired end. We ran STAR it with these parameters (for ...
written 4.7 years ago by Paolo Guarnieri20
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Answer: A: SGSeq error on analyzeFeatures
... Hi Leonard,   thanks for your reply.  You are right: my paired end reads were aligned with "olego" (wu et al. 2013 NAR) and the reads were treated as individual single ends and not as paired. And yes, it does not have that tag. It was not clear to me, that tag was necessary, and even if it was c ...
written 4.7 years ago by Paolo Guarnieri20
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Answer: A: SGSeq error on analyzeFeatures
... Hi Leonard, thanks for your reply. Unfortunately the chr is not the issue, or at least for I what I could check. I made sure it was in the right format. I checked BAM and annotation (that is why I removed the "NCBI" line). That was one of the things Brad recommended to check. I can compile a self ...
written 4.7 years ago by Paolo Guarnieri20
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SGSeq error on analyzeFeatures
... Dear all, I am trying to test SGSeq with my own data, but I did not go that far: I am simply trying to get your package working on a test set composed of 8 bam files (paried end) merged into 4, subset to only one chromosome. Also the annotation is subset accordingly. I get an obscure "non-numeric ...
splicing sgseq analyzefeatures written 4.7 years ago by Paolo Guarnieri20
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gene set enrichment analysis of RNA-Seq data
... Dear Gordon, Thank you very much for your detailed explanations and clarifications. Very useful. Thanks, Paolo -----Original Message----- From: Gordon K Smyth [mailto:smyth@wehi.EDU.AU] Sent: Saturday, April 28, 2012 22:38 To: Paolo Guarnieri Cc: Bioconductor mailing list Subject: gene set enric ...
microarray limma glad edger goseq written 7.3 years ago by Paolo Guarnieri20
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Answer: A: gene set enrichment analysis of RNA-Seq data
... Gordon K Smyth writes: > > Dear Julie, > > A good question. As far as I know, there is as yet no such method. What > I am doing for this purpose for the time being is to use voom() in the > limma package to transform the RNA-Seq counts to a scale on which > microarray methods ...
written 7.3 years ago by Paolo Guarnieri20

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Popular Question 4.7 years ago, created a question with more than 1,000 views. For gene set enrichment analysis of RNA-Seq data

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