User: daniele.avancini

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Posts by daniele.avancini

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Correlation matrix between enhancers and promoters (human)?
... I've spoken directly to the curators of the FANTOM5 database and they directed me to the source of the file. To whom it may concern, this is the link to enhancer-promoter correlation matrix I was talking about: [http://slidebase.binf.ku.dk/human_enhancers/presets][1] [1]: http://slidebase.binf. ...
written 8 weeks ago by daniele.avancini10
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Comment: C: Correlation matrix between enhancers and promoters (human)?
... Thanks, @geek_y. That was one of the paper I took information from but it wasn't the source of my file. ...
written 8 weeks ago by daniele.avancini10
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Correlation matrix between enhancers and promoters (human)?
... Dear all, I need your help in finding a file I downloaded while ago but I cannot find anymore online. The file is a correlation matrix between enhancer and promoters calculated as described in An atlas of active enhancers across human cell types and tissues (Andersson et al, 2014). The file is co ...
enhacer promoters correlation cage written 8 weeks ago by daniele.avancini10
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Diffbind for ATAC-seq data with no controls
... Hi all, I'm trying to use Diffbind to identify differentially open regions (identified using ATAC-seq) between three different cell types. I have three biological replicates for each cell type. I'm building now the sample sheet to import the data into Diffbind, but I don't know what I should indica ...
diffbind atac-seq written 10 months ago by daniele.avancini10 • updated 10 months ago by Rory Stark500
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Comment: C: Mitochondrial contamination over 90% in published atac-seq dataset.
... Thanks ATPoint for sharing with me your script, I'll definitely use that in the future. I did no calculation, to be honest, I just filtered the bam file for chrM tags and I was left with less than 10% of the mapped reads. Still don't know what I'm doing wrong with those files, don't know if is a map ...
written 13 months ago by daniele.avancini10
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Comment: C: Mitochondrial contamination over 90% in published atac-seq dataset.
... The new analysis using bowtie instead of bowtie2 gave a bit better results with an average MT mapping around 80%. Still high, but is the best I could get and I don't really know where I find this discrepancy in the data. I will call the peaks anyway and see what happens. Do you have any further sug ...
written 15 months ago by daniele.avancini10
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Comment: C: Mitochondrial contamination over 90% in published atac-seq dataset.
... Thank again, I will post the results of the new analysis. ...
written 16 months ago by daniele.avancini10
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Comment: C: Mitochondrial contamination over 90% in published atac-seq dataset.
... Questioning published results wasn't the purpose of my query at all, in fact, I'm pretty sure that the problem is at my end. I used two different aligners obtaining similar results. But you pointed out something solid and I'll use bowtie v.1 to perform the alignments. Thank for your reply. ...
written 16 months ago by daniele.avancini10
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Mitochondrial contamination over 90% in published atac-seq dataset.
... Hi all, I know this topic has been touched in the past but I couldn't find an answer to my question. Background: in my lab, we are thinking to move from chip-seq of histone marks to atac-seq. We have data on CD4+ T cells and we would like to compare what we found with an already published dataset i ...
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Comment: C: setting Coldata levels in Deseq2
... May I ask what would you expect from `colData(ddHTSeq)`? I guess in the factor column you should have if the sample received or didn't receive the chemical gossypol. Right? Also, your code above is missing a `)` at the end of colData. ...
written 17 months ago by daniele.avancini10

Latest awards to daniele.avancini

Scholar 8 weeks ago, created an answer that has been accepted. For A: Correlation matrix between enhancers and promoters (human)?
Popular Question 6 months ago, created a question with more than 1,000 views. For Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
Popular Question 6 months ago, created a question with more than 1,000 views. For Mitochondrial contamination over 90% in published atac-seq dataset.

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