User: hkarakurt

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hkarakurt30
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2 months ago
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1 year, 7 months ago
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Posts by hkarakurt

<prev • 29 results • page 1 of 3 • next >
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newSCESet and SingleCellExperiment basic differences and TMM Normalization
... Hello everyone, I am trying to replicate a single cell RNA-Seq data analysis. Actually, the main problem is version. The old results were generated via newSCESet and normalized with normaliseExprs command (TMM method) but for the newest version of R, Bioconductor and packages so I used SingleCellEx ...
single-cell R rna-seq written 9 weeks ago by hkarakurt30
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Enrichment Tool for Mouse miRNAs
... Hello everyone, I am looking for a tool to do miRNA enrichment analysis. I have found many tools but they only accept human microRNAs but I need this tool for Mus musculus. Are there any tools like that? Thank you. ...
enrichment go analysis mirna written 5 months ago by hkarakurt30
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Annotation File for Enchancer Regions in Ensembl mm10 genome
... Hello everyone, I analyzed a ChIP-Seq Data (H3K4me1 and H3K27ac) and I need an enhancer annotation file (GFF/GTF) to use in SeqMonk. Is there any annotation file for enhancers? Thank you. ...
enhancer chip-seq written 5 months ago by hkarakurt30
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Hisat2 or Bowtie2 for ChIP-Seq Data?
... Hello everyone, I am analyzing a ChIP-Seq data and I aligned them with Bowtie2 with default parameters. I used to use Hisat2 for my RNA-Seq data but I heard Bowtie2 gives better results with short reads. Actually a friend said that I have done the alignment step but I need to be sure. Is Bowtie2 ...
alignment chip-seq sequencing written 6 months ago by hkarakurt30 • updated 6 months ago by EagleEye6.0k
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Answer: A: Genes with promoter and enhancer regions as GTF
... Thank you for answers. I will explain more clearly and tell the reasons. I used MACS for peak calling. I also have BAM files I just forgot to mention that. I used featureCounts to quantify my peaks. I used GTF file as annotation. I have 7 samples for H3K4me1 and 6 samples for H3K27ac ChIP-Seq exper ...
written 6 months ago by hkarakurt30
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Genes with promoter and enhancer regions as GTF
... Hello, I am doing a ChIP-Seq analysis and I have sorted SAM files (I used MACS). I used featureCounts and GTF file from USCS Table Browser. I have chosen "Genes and Gene Predictions" as group, "UCSC Genes" as track and "knownGene" as table. Now I have Counts matrix for my ChIP-Seq experiments and I ...
gtf chip-seq genes featurecounts promoter written 6 months ago by hkarakurt30
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Differential ChIP-Seq Analysis
... Hello everyone, I have ChIP-Seq datasets. With Bowtie2, now I have BAM files. I mostly use SeqMonk for these kind of analyses but I do not think it does not have a tool for differential ChIP-Seq analysis. I used MACS for peak calling (on SeqMonk) and I have values too. 1) Anyone knows a suitable an ...
R next-gen chip-seq alignment written 7 months ago by hkarakurt30 • updated 7 months ago by igor7.1k
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Comment: C: How to extrach gene names and peaks from BedGraph or BigWig files
... Thank you for your help. I think I should start from raw data to have better result. ...
written 7 months ago by hkarakurt30
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Comment: C: How to extrach gene names and peaks from BedGraph or BigWig files
... I am using deepTools now (on Galaxy Server) and compare the BigWig files then my plan is to visualize them in IGV but the problem is my BigWig files does not include any gene information. I am not sure what should I do now. ...
written 7 months ago by hkarakurt30
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How to extrach gene names and peaks from BedGraph or BigWig files
... Hello everyone, I have BigWig files from a ChIP-Seq experiment. I need to find the differences between the two tissues. How can I find the information like differentially changed genes with p-values or fold changes of peaks between two tissues? Maybe a desktop app to visualize my files can work. I ...
peak bedgraph chip-seq bigwig written 7 months ago by hkarakurt30 • updated 7 months ago by Devon Ryan86k

Latest awards to hkarakurt

Popular Question 6 months ago, created a question with more than 1,000 views. For Retrieving data from NCBI GEO and RNA-Seq Data Analysis
Popular Question 8 months ago, created a question with more than 1,000 views. For Retrieving data from NCBI GEO and RNA-Seq Data Analysis

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