User: samuel collombet

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France
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Posts by samuel collombet

<prev • 43 results • page 1 of 5 • next >
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fourCseq - error getZscores
... Hi, When I try to call the function getZSCores on my 4C data (mouse) I got the following error: > data_fcf <- getZScores(data_fc,minCount=10,fitFun=distFitMonotone) [1] "VP1" gene-wise dispersion estimates mean-dispersion relationship NOTE: fitType='parametric', but the dispersion trend was ...
fourcseq written 2.0 years ago by samuel collombet100 • updated 22 months ago by felix.klein140
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Comment: C: ChIPseq-style peak calling for paired-end sequencing?
... Thanks Gordon! In the case of ATAC we do not have a background/input to compare to (like DNAse), but I could use the method of filtering by local enrichment you propose in the csaw user guide, to mimic peak calling. Thanks! ...
written 2.5 years ago by samuel collombet100
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Comment: C: ChIPseq-style peak calling for paired-end sequencing?
... In the original paper describing ATACseq, they used ZINBA. In fact macs2 works very well on our data, but I was wodnering if something in R existed that would handle paired end :) ...
written 2.5 years ago by samuel collombet100
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Comment: C: Merge multiple genomic intervals if overlapping more than xx percents
... Basically I want to make a unique annotation of enriched regions, based on multiple ChIPseq experiment (I get enriched regions for each regions using macs for peak calling). For now I just merge any overlapping regions from any experiments ; However, I have found that some times, I can find 2 peaks ...
written 2.5 years ago by samuel collombet100
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Comment: C: Merge multiple genomic intervals if overlapping more than xx percents
... Thanks Michael! So the only way to merge overlap ranges from my 4 (or more) granges, is to perform all the pairwise comparison? My problem is: if I have a range a in A that overlap a range b in B (with more than 60%), and a also overlap (>60%) a range c in C, I want then to merge then all into o ...
written 2.5 years ago by samuel collombet100
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Merge multiple genomic intervals if overlapping more than xx percents
... Hi, I have multiple set of genomic intervals (peaks from ChIPseq, at least 4 set of several 1000s of intervals), and I would like to merge them into one unique set of interval, where intervals overlapping are fused, if the overlap is more than 60% of the length of one of them.  I guess I should be ...
genomicranges written 2.5 years ago by samuel collombet100 • updated 2.5 years ago by Hervé Pagès ♦♦ 13k
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Comment: C: ChIPseq-style peak calling for paired-end sequencing?
... from https://groups.google.com/forum/#!searchin/macs-announcement/BAMPE/macs-announcement/Vh916L3tOOE/TUjLeQtsCfkJ : "In BAMPE mode, the 5’ end plus the observed template length will both be recorded so in later analysis, MACS2 piles up the actual entire observed fragment/template instead of estimat ...
written 2.5 years ago by samuel collombet100
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Comment: C: ChIPseq-style peak calling for paired-end sequencing?
... I might have misunderstood something, but I think that macs2 in mode BAMPE do take the fact that data are paired-end into account (extending reads to the fragment length in the bam file, not an average fragment length). ...
written 2.5 years ago by samuel collombet100
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ChIPseq-style peak calling for paired-end sequencing?
... Hi, I was wondering of there was any package implementing a peak calling method that would take paired-end data (for ATACseq precisely).  I am checked the packages narrowPeaks, BayesPeaks and SPP (which is not in bioconductor), but none seems to work with paired-end data. I am currently using macs ...
dnaseq chipseq bayespeak narrowpeaks atac written 2.5 years ago by samuel collombet100 • updated 2.5 years ago by Gordon Smyth32k
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Comment: C: featureCounts - paired-end data
... For the use of STAR for ChIPseq (or genomic DNA in general), I think I am not the only one who tried (see https://groups.google.com/forum/#!topic/rna-star/E_mKqm9jDm0). I compared STAR mapping to bowtie2 and got quite similar results (in therm of mapping efficiency, signal  correlation and enriched ...
written 2.5 years ago by samuel collombet100

Latest awards to samuel collombet

Popular Question 12 months ago, created a question with more than 1,000 views. For limma - F-test for many condition
Popular Question 12 months ago, created a question with more than 1,000 views. For ChIPseq-style peak calling for paired-end sequencing?
Popular Question 21 months ago, created a question with more than 1,000 views. For ChIPseq-style peak calling for paired-end sequencing?
Popular Question 21 months ago, created a question with more than 1,000 views. For featureCounts - paired-end data
Popular Question 21 months ago, created a question with more than 1,000 views. For ChIPseq-style peak calling for paired-end sequencing?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For DESeq2 - paired sample, interaction and fold change
Student 2.5 years ago, asked a question with at least 3 up-votes. For ChIPseq-style peak calling for paired-end sequencing?

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