User: hamza_karakurt

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2 months ago
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1 year, 9 months ago
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h*************@windowslive.com

Posts by hamza_karakurt

<prev • 8 results • page 1 of 1 • next >
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Output Files of MACS2 bdgdiff
... Hello everyone, I have some bedgraph files from a ChIP-Seq experiment (2 replicates for each condition) and I used BDGDiff tool to find differential peaks. It needs 4 bedgraph files so I gave 2 replicates for 2 conditions and now I have 3 out files in bed format, Condition 1 (19,960 regions), Condit ...
chip-seq macs2 bed bedgraph written 3 months ago by hamza_karakurt10 • updated 3 months ago by Jennifer Hillman Jackson25k
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Extracting Gene Names from BigWig File
... Hello, I have some BigWig files of a ChIP-Seq analysis. I used BigWig compare in Galaxy but I don't know how to find names of differential changed genes. Is there any tool for this in Galaxy? Or which external tool should I use? Thank you. ...
chip-seq bigwig deeptools written 3 months ago by hamza_karakurt10 • updated 3 months ago by Devon Ryan1.9k
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(Closed) How to make negative values positive for t-test
... Hello everyone, I have an microarray data and I want to use volcanoplot (with t-test) in Matlab but it does not include negative values to the plot. I want to make negative values positive. How can I do that? Adding mean to each gene's data works? Thank you. ...
transcriptome matlab t-test data microarray written 7 months ago by hamza_karakurt10
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Finding gene names from TopHat results.
... Hello, I am trying a build a workflow for RNA-Seq analysis and I want to verify my methods via comparing a data set. The data sets I am trying to use are GSE56016 and GSE36537 from NCBI GEO. They have only one RNA-Seq result. I downloaded fasta from EBI SRA did analysis. I used TopHat and want to co ...
bam genenames bed tophat written 9 months ago by hamza_karakurt10 • updated 9 months ago by Jennifer Hillman Jackson25k
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Comment: C: Local Galaxy. Trimmomatic does not see fastq files.
... Here is the screenshot of my history. Files are in fastqsanger format. https://imgur.com/a/6HL3f ...
written 10 months ago by hamza_karakurt10
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Comment: C: Local Galaxy. Trimmomatic does not see fastq files.
... Data sets assigned as fastqsanger. I have no idea why I have this kind of error. Thank you for your interest. ...
written 10 months ago by hamza_karakurt10
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Local Galaxy. Trimmomatic does not see fastq files.
... Hello, I am new at Galaxy and trying to use it both local and in server. I downloaded some tools to local and tried to do an RNA-seq analysis. I tried to do this tutorial https://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise In Galaxy Server, It is working actually but when I try it on ...
trimming fastq quality trimmer fastq rna-seq written 10 months ago by hamza_karakurt10 • updated 10 months ago by zachary.gaber80
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About CHIP Seq Data Download
... Hello, I am a new learner in bioinformatics tools and want to learn how analyze chip seq data in Galaxy. I need to find a adipose stem cell chip seq data file (if there are any) but I have no idea where to find chip seq analysis results. Do you know any good databases? ...
chip-seq resources data written 21 months ago by hamza_karakurt10 • updated 21 months ago by Jennifer Hillman Jackson25k

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