User: Eric Fournier

gravatar for Eric Fournier
Eric Fournier1.4k
Reputation:
1,390
Status:
Trusted
Location:
Quebec, Canada
Last seen:
4 years, 11 months ago
Joined:
8 years, 1 month ago
Email:
e**************@ulaval.ca

Posts by Eric Fournier

<prev • 95 results • page 1 of 10 • next >
16
votes
2
answers
2.3k
views
12 follow
2
answers
Seeking practical advice for choosing an algorithm for performing GO enrichment.
... The most common way of performing GO enrichment (hypergeometric tests on selected subsets of genes) is straightforward enough, but I'm finding a lot of papers which propose alternate methods which take into account the hierarchy of GO terms or gene scores: Cao & Zhang, 2014, A Bayesian Extensio ...
enrichment forum microarray go written 5.0 years ago by Eric Fournier1.4k • updated 2.8 years ago by prasadhendre20
0
votes
2
answers
14k
views
2
answers
Comment: C: Normalizing Rna-Seq Data Using Ercc Spike-In
... I haven't been using cuffdiff for differential expression testing, as it has been crashing when I try to feed it 30 multi-gb bam files at a time. ...
written 5.8 years ago by Eric Fournier1.4k
0
votes
2
answers
14k
views
2
answers
Comment: C: Normalizing Rna-Seq Data Using Ercc Spike-In
... I've tried using loess for normalization, but the results have been pretty awful. I cannot say with certitude why this issue arises, but I think it might be because in my data, the ERCC concentration - FPKM correlation goes down the drain at lower concentrations, with FPKMs that sometime vary by a h ...
written 5.8 years ago by Eric Fournier1.4k
11
votes
2
answers
14k
views
8 follow
2
answers
Normalizing Rna-Seq Data Using Ercc Spike-In
... Hi, I have sequencing data which has been spiked-in with exogenous ERCC controls to allow normalization. I have aligned the reads using tophat 2, and evaluated their abundance using cufflinks. To normalize transcript abundances and get a measure which is directly comparable between replicates, my s ...
normalization fpkm rna-seq written 5.9 years ago by Eric Fournier1.4k • updated 5.9 years ago by Devon Ryan91k
6
votes
2
answers
2.7k
views
2
answers
Simple Tool For Finding Known Regulatory Motifs In A Single (Eukaryotic) Sequence
... I'm looking for a motif/regulatory sequence finding tool to recommend to the wet-lab scientists I work with. Are there any simple, user-friendly tools which take a single sequence and find known regulatory motifs (TFBS, TATA-boxes, etc.) within it? The tools I've seen being recommended here all seem ...
motif database search written 6.6 years ago by Eric Fournier1.4k • updated 5.5 years ago by Biostar ♦♦ 20
0
votes
1
answer
1.5k
views
1
answers
Answer: A: Most Appropriate Analysis For Population Specific Genotype Frequencies
... I've found that the article Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples and the software EM-SNP provided all of the information necessary to determine how to best analyze my data. ...
written 6.6 years ago by Eric Fournier1.4k
0
votes
1
answer
1.5k
views
1
answers
Comment: C: Most Appropriate Analysis For Population Specific Genotype Frequencies
... What I mean is that I have population specific variant frequencies (For example, I know that at position X of chromosome Y, 25% of population A has a C->T SNP while only 12% of population B has the same SNP), but I have no haplotypes (IE given loci A, B and C with allelles Aa, Bb and Cc, I cannot ...
written 6.7 years ago by Eric Fournier1.4k
4
votes
1
answer
1.5k
views
1
answer
Most Appropriate Analysis For Population Specific Genotype Frequencies
... Our group is trying to find new genomic variants associated with a certain phenotypic trait. To do so, we performed DNA capture of regions of interest (~5Mb) on ~10 individuals for each of the populations of interest. We then pooled the DNA and performed two separate sequencing runs. Now, I've alig ...
sequencing association genotyping written 6.7 years ago by Eric Fournier1.4k
0
votes
2
answers
4.5k
views
2
answers
Comment: C: Generating Multiple Species Alignment Of Novel Transcripts For Phylocsf
... Here's what I ended up doing, in a nutshell: 1. Get species-to-species alignments from the UCSC Genome Browser (Cow to mouse, Cow to Dog, Cow to human, etc.) in axt format. 2. Convert from axt to MAF format using the axtToMaf tool from the kent source tree (Again, from the UCSC Genome Browser) 3. Sp ...
written 6.7 years ago by Eric Fournier1.4k
11
votes
2
answers
3.4k
views
5 follow
2
answers
Comparative Network Visualization
... I know tools like BioLayout allow me to visualize gene networks. However, are there any tools out there that allow the comparative visualization of networks? I'm thinking of something like this: IE, given two gene network, I want to easily visualize which nodes are only in one of the two network ...
network visualization comparative written 6.9 years ago by Eric Fournier1.4k • updated 6.9 years ago by enricoferrero770

Latest awards to Eric Fournier

Voter 5.8 years ago, voted more than 100 times.
Guru 5.8 years ago, received more than 100 upvotes.
Student 5.8 years ago, asked a question with at least 3 up-votes. For When And Why Should Short 454 Reads Be Discarded?
Popular Question 5.8 years ago, created a question with more than 1,000 views. For In Bowtie2'S Sam Output, What Does The Yt Attribute Mean?
Popular Question 5.8 years ago, created a question with more than 1,000 views. For Normalizing Rna-Seq Data Using Ercc Spike-In
Supporter 5.8 years ago, voted at least 25 times.
Student 5.9 years ago, asked a question with at least 3 up-votes. For Normalizing Rna-Seq Data Using Ercc Spike-In
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Normalizing Rna-Seq Data Using Ercc Spike-In
Student 6.9 years ago, asked a question with at least 3 up-votes. For Comparative Network Visualization
Commentator 7.2 years ago, created a comment with at least 3 up-votes. For C: Working Out The Number Of Introns In A Gene Given The Number Of Exons
Teacher 7.3 years ago, created an answer with at least 3 up-votes. For A: What Tools Are Available For Analyzing Bisulfite Data?
Teacher 7.4 years ago, created an answer with at least 3 up-votes. For A: Are Coding Region Sequences Generally More Conserved Than Non-Coding Region Sequ
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: Blast Result Matching Both Of Two Query Sequences?
Appreciated 7.5 years ago, created a post with more than 5 votes. For C: C And Fortran Programming Language
Commentator 7.5 years ago, created a comment with at least 3 up-votes. For C: C And Fortran Programming Language
Student 7.7 years ago, asked a question with at least 3 up-votes. For Fully Automated And Integrated Sequence Analysis
Appreciated 7.7 years ago, created a post with more than 5 votes. For Fully Automated And Integrated Sequence Analysis
Student 7.8 years ago, asked a question with at least 3 up-votes. For Guide To Working With Repeated Elements
Appreciated 7.8 years ago, created a post with more than 5 votes. For Guide To Working With Repeated Elements
Good Question 7.8 years ago, asked a question that was upvoted at least 5 times. For Guide To Working With Repeated Elements
Commentator 7.9 years ago, created a comment with at least 3 up-votes. For C: Why Do You Want To Work In This Lab?
Teacher 7.9 years ago, created an answer with at least 3 up-votes. For A: Sequence Comparison Using Python/Biopython
Teacher 8.0 years ago, created an answer with at least 3 up-votes. For A: Where Can I Find A Good Database Of The Repeat Regions Of The Human Genome ?
Teacher 8.1 years ago, created an answer with at least 3 up-votes. For A: Rna Sequencing Vs Beadarray/Microarray
Good Answer 8.1 years ago, created an answer that was upvoted at least 5 times. For A: Rna Sequencing Vs Beadarray/Microarray

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1445 users visited in the last hour