User: firatuyulur

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firatuyulur190
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Posts by firatuyulur

<prev • 38 results • page 1 of 4 • next >
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Normalizing count data with several treatment dosages
... Hi, My experimental setup is as; 3 plates, each plate contains treatment of a chemical in 6 different dosages and a control.The duration of the treatment is the same across all dosages. The sequencing is done via bioSpyder, where each gene is represented by a 50bp probe, so you sequence a ~unique p ...
normalization deseq2 qc rna-seq edger written 12 weeks ago by firatuyulur190
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Comment: C: plotting an expression data in heat map/ hierarchical clustering
... I feel like heatmap would be better as clustering methods would not give any idea of up/downregulation, and also you can cluster your samples while plotting the heatmap. ...
written 3 months ago by firatuyulur190
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Answer: A: ATAC-seq: differential peaks using macs2 bdgdiff yields strange results
... I was working with MACS2 a lot last year and had similar issues. I cannot give a straight answer to this question but while calling my peaks from bam files I remember using `-B --SPMR` which asks MACS2 to generate pileup signal file of 'fragment pileup per million reads' in bedGraph format. Then you ...
written 3 months ago by firatuyulur190
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comparing DEGs with same treatment but different control batch
... Hi, Its sound quite trivial but I couldnt find the way somehow. I have an RNASeq with 3 replicates of treatment and 9 controls. As I noticed something strange with controls looking at their raw counts by eye, I normalised and clustered them. They clustered in 3 different groups. Even this tells me ...
deseq2 correlation rna-seq statistics written 3 months ago by firatuyulur190 • updated 3 months ago by swbarnes23.6k
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Answer: A: Filter by Fold change in DESeq2
... There is a function, complete.cases(), in R that helps you to get rid of NAs. mydata[complete.cases(mydata),] will give you your dataframe with no NAs. Then you can apply any numeric filtering you like. ...
written 9 months ago by firatuyulur190
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Comment: C: Optimization of RNA-Seq data mapping with tophat2
... Last time i had scores like this, i tried trimming according to fastqc results and it improved the numbers a lot. ...
written 9 months ago by firatuyulur190
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Answer: A: From bam files to isoform read counts
... Try [sailfish][1] They are not the exact counts but would work for many purposes. [1]: http://www.cs.cmu.edu/~ckingsf/software/sailfish/ ...
written 10 months ago by firatuyulur190
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Comment: C: macs2 normalization on broadPeak
... James thanks for the help. After this quick conversation I started looking at the regions of peaks on igv. I put the spmr called bedgraphs to igv and checked broadpeaks beds by eye. Still cannot strongly argue about it, I suppose you are right about peak calling normalizes while doing its job. ...
written 10 months ago by firatuyulur190
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Comment: C: macs2 normalization on broadPeak
... Isnt fold change related to the number of reads aligned to the peak? ...
written 10 months ago by firatuyulur190
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Comment: C: macs2 normalization on broadPeak
... So what you are saying is the signalValues that I see in broadPeaks file are independent of the read depth as those are the values obtained from a normalised peak calling and I can compare two samples according to their signalValues although they have different read depths? ...
written 10 months ago by firatuyulur190

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Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Is It Fastq Format

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