User: ahnje770

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ahnje7700
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Posts by ahnje770

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Dealing with multimapped reads with Chip-seq and ATAC-seq data when studying Transposable Elements
... I was wondering about the methods that deal with multi mapping reads when investigating transposable elements (TE) with ChiP-seq and ATAC-seq data. Many publications remove reads that map to multiple genomic regions however TE’s from younger families are more likely to have multi mapping reads given ...
transposable elements chip-seq atac-seq written 11 weeks ago by ahnje7700
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Outliers Detection with Cook's distance
... I have made a list of differentially expressed genes with DESeq2. However i find that when i look at the normalised count (using rlog) of these top genes, they are commonly affected by outliers or there doesn't seem to be consistent gene expression changes between the 2 groups. My desgin is 4 sample ...
deseq2 rna-seq written 4.3 years ago by ahnje7700
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Getting a Count Matrix from GEO for RNA-eq
... Hi, Could anyone help me get some sort of a count matrix when processed RNA-seq data is extracted from GEO. I have some experience using microarray data from GEO. For example, for GSE78220, the data has been processed by: "FASTQ files were mapped by Tophat2 Tophat BAMs were quantified and norm ...
rna-seq written 4.4 years ago by ahnje7700 • updated 4.4 years ago by GZ1995380

Latest awards to ahnje770

Popular Question 4.3 years ago, created a question with more than 1,000 views. For Getting a Count Matrix from GEO for RNA-eq
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Outliers Detection with Cook's distance

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