User: hkarakurt
hkarakurt • 20
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Posts by hkarakurt
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... 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 ...
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... 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
hkarakurt • 20
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... 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 ...
written 12 days ago by
hkarakurt • 20
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... 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 ...
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139
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... Thank you for your help. I think I should start from raw data to have better result. ...
written 7 weeks ago by
hkarakurt • 20
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... 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
hkarakurt • 20
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... 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 ...
written 7 weeks ago by
hkarakurt • 20
• updated
7 weeks ago by
Devon Ryan ♦ 80k
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... 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
hkarakurt • 20
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... With cost I mean edge weight. ...
written 11 weeks ago by
hkarakurt • 20
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167
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... 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 ...
written 11 weeks ago by
hkarakurt • 20
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