User: atsalaki

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atsalaki10
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2 years, 10 months ago
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Posts by atsalaki

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Pvalue in annotated peak files
... Iam new to the field. I have annotated a chip-seq data bed peak file from ENCODE by taking the nearest to TSS genes in 5000 distance. From 50.000 records of the bed file i finaly found 1.500 records, genes that are upstream of the genes near TSS. These records have pvalues and qvalues. I wonder is i ...
pvalue cut-off chip-seq written 2.9 years ago by atsalaki10
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Is there a different gene id(e.g symbol name) for a gene's exon , a gene's intron , a gene's promoter?
... Is there a different gene id(e.g symbol name) for a gene's exon , a gene's intron , a gene's promoter? ...
gene written 2.9 years ago by atsalaki10 • updated 2.9 years ago by Sinji2.8k
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ENOCDE peaks files p-value
... I downloaded peak files from ENCODE Chip-seq matrix of cell line MCF7 and TF CTCF. they have a column q-value that is the FDR, i assumed ..... Is it correct to calculate the p-value missing column values(all values are -1 because they are not provided )with this approach or it has no meaning for th ...
p-value chip-seq q-value written 2.9 years ago by atsalaki10
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Comment: C: Small percentage of overlapping chip-seq peaks
... All the chromosomes , no distance computed venny it just takes the unique entries from the two lists and correlates them to see how they fit. ...
written 2.9 years ago by atsalaki10
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Comment: A: Small percentage of overlapping chip-seq peaks
... All the chromosomes , no distance computed venny it just takes the unique entries from the two lists and correlates them to see how they fit. ...
written 2.9 years ago by atsalaki10
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After Annotation in R , the binding sites are less than the starting downloaded from ENCODE Chip-seq Matrix
... I download ENCODE chip-seq broadpeak files and annotate them in R with annotatePeakInBatch(gr_narrowPeak, featureType = c("TSS"),maxgap=5000 ,AnnotationData=annotationData , output="overlapping", FeatureLocForDistance="TSS") .The binding sites i get are less that the starting in the ENCODE peak fil ...
peaks chip-seq written 2.9 years ago by atsalaki10
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Small percentage of overlapping chip-seq peaks
... I have downloaded ENCODE chip-seq peaks for HepG2 cell line with FOXA2(TF). I found this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2794179/#!po=21.4286 i took the chip-seq data for HepG2 in FOXA2 they have in this paper I used venn diagramm to find the overlapping peaks and for my suprise ...
chip-seq written 2.9 years ago by atsalaki10 • updated 2.9 years ago by igor8.1k
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Answer: A: How to install R pachages in R studio - UBUNTU 16.4 Linux Without ERROR
... Try this http://askubuntu.com/questions/386887/install-curl-ubuntu-12-04 it worked for me months ago ...
written 2.9 years ago by atsalaki10
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Chip-seq Binding sites
... Where can i find chip-seq peak files except ENCODE for various Transcription factors in various cell lines(e.g. i am looking CTCF with MCF7 binding sites)? Iam looking for files with hundreds or thousands of genes. ...
chip-seq binding-sites written 2.9 years ago by atsalaki10 • updated 2.9 years ago by Denise - Open Targets5.0k
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Differentiall analysis of chip-deq data
... I am new to genetics study , i dont completely understand what differentialy analysis of chip-seq data means .Whats the meaning of differentially binding sites in simple words, whats the meaning of word differentiall in biology?Can someone help?Thanks in advance! ...
differentiall chip-seq written 3.0 years ago by atsalaki10 • updated 3.0 years ago by Satyajeet Khare1.4k

Latest awards to atsalaki

Supporter 3.0 years ago, voted at least 25 times.
Scholar 3.0 years ago, created an answer that has been accepted. For A: Binding sites of annotated chip-seq peak files

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