User: hkarakurt

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hkarakurt20
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Posts by hkarakurt

<prev • 26 results • page 1 of 3 • next >
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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 days ago by hkarakurt20 • updated 6 days ago by EagleEye5.3k
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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 12 days ago by hkarakurt20
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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 12 days ago by hkarakurt20
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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 6 weeks ago by hkarakurt20 • updated 6 weeks ago by igor6.2k
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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 weeks ago by hkarakurt20
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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 weeks ago by hkarakurt20
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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 weeks ago by hkarakurt20 • updated 7 weeks ago by Devon Ryan80k
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Comment: C: Where to download Protein-Protein Interaction Network with Cost values (Or Calcu
... Thank you for your answer. The "cost" they gave is between 0 and 1. Probably they normalized it. Also, I downloaded coexpression network from GeneMania database and it has its own scores (About 12 million interactions actually so it is hard to manipulate). I hope with cost they meant edge weight. ...
written 11 weeks ago by hkarakurt20
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Comment: C: Where to download Protein-Protein Interaction Network with Cost values (Or Calcu
... With cost I mean edge weight. ...
written 11 weeks ago by hkarakurt20
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Where to download Protein-Protein Interaction Network with Cost values (Or Calculate)?
... Hello everyone, I need to build a protein-protein interaction network (Mus musculus) with costs. Actually I will use this interaction network for PCSF package of R. I checked STRING data base. I downloaded Mus musculus data and it has a combined score column. Is it same with cost? Also all protein ...
ppi string network written 11 weeks ago by hkarakurt20

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Popular Question 10 weeks 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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