User: anais1396

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anais139620
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Brussels
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9 months ago
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2 years, 4 months ago
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Posts by anais1396

<prev • 22 results • page 1 of 3 • next >
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Processing ATAC-seq data after peak calling
... Hello everyone !! I've started to work on ATAC-seq data and I would like to know how to process data after peak calling ? I've two group to study, patients and healthy control, and after performing peak calling to see regions of open chromatin (that correspond to genes potentially expressed), I w ...
peak calling sequencing written 14 months ago by anais139620 • updated 12 months ago by phosphodiester_bond30
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Multiple ways to make an IntersectBed on bed file after peak calling : which one is the good one ??
... Hello Biostars !! I have .bed files resulting from Macs peak calling that are biological replicates. I have 5 replicates for healthy people and 6 for patients. I merged the 5 samples to a set for healthy represented in one file and I made the same for the patients so I have one bed file for all the ...
peak calling ngs intersect written 14 months ago by anais139620 • updated 14 months ago by ATpoint21k
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Comment: C: Comparison of replicates from NGS : merge before or after peak calling ?
... How can I simply check the coverage of my samples ? ...
written 14 months ago by anais139620
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Comparison of replicates from NGS : merge before or after peak calling ?
... Hello everyone !! I have a question for you : I have biological replicates from Atac-seq experience and I want to perform a peak calling and then a comparison of the overlaps between my files. I have 5 samples for healthy people and 9 samples for patients and I have 2 strategies : - first, I hav ...
peak calling ngs merge written 14 months ago by anais139620 • updated 14 months ago by h.mon27k
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Comment: C: BED file : error in naming chromosome's column
... Sorry, I forgot !! It's now done ...
written 14 months ago by anais139620
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Comment: C: BED file : error in naming chromosome's column
... Thank you very much !! It solves my problem !! ;-) ...
written 14 months ago by anais139620
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Comment: C: ATAC-seq : strategies to have the list of the expressed genes
... Thank you !! It's very helpful !! ...
written 14 months ago by anais139620
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BED file : error in naming chromosome's column
... Hello everyone !! I have a problem with the chromosome's column in my BED files and I'll try to explain that. I have bed files from a peak calling (in format narrowPeak) and in the column chr, we have just the number of the chr that is writting and we need 'chr+the number of the chr' writting. Le ...
bed ngs written 14 months ago by anais139620
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Comment: A: ATAC-seq : strategies to have the list of the expressed genes
... I tried to load required packages but it doesn't work... I have the following error message :"installation path not writeable, unable to update packages: MASS, survival" for the loading of bioclite() and then I have this "installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exi ...
written 14 months ago by anais139620
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Comment: C: ATAC-seq : strategies to have the list of the expressed genes
... Thank you very much for your answer, it is very helpful !! Where do you have the files with the promoters in R? I will also need them with the hg38 version of the human genome Or maybe just in switching the hg19 into hg38 in the name of the file in R ?? ...
written 15 months ago by anais139620

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Popular Question 14 months ago, created a question with more than 1,000 views. For Normalization and differential analysis in ATAC-seq data

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