User: firatuyulur

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firatuyulur250
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Posts by firatuyulur

<prev • 43 results • page 1 of 5 • next >
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Answer: A: equal distance between groups in a barplot
... I just [read][1] now that there is a parameter called "space" in barplot function. for each bar, you type the distance from the next bar. [1]: https://stackoverflow.com/questions/13932708/how-do-i-control-space-between-bars ...
written 12 weeks ago by firatuyulur250
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Comment: C: removing outliers before running DESeq2
... Why do you think you need to remove outliers? I tend to remove the genes that doesnt have more than 5 counts on average across all samples but nothing more. ...
written 12 weeks ago by firatuyulur250
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Comment: C: size of the pathways for analysis and filtration
... There is a p-value, based on fisher exact two tailed test, and even after filtration there is a good number of small pathways coming out as significant. I put the same question to stack and was suggested to do [multiple comparisons][1] yet I do not know how to do it on such data as it is the tool do ...
written 3 months ago by firatuyulur250
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Answer: A: rRNA remove from RNAseq data
... I have used [SortMeRNA][1] before and worked very well for me. [1]: http://bioinfo.lifl.fr/RNA/sortmerna/ ...
written 3 months ago by firatuyulur250
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size of the pathways for analysis and filtration
... Hi, I have recently started working on a substance's effect on a cell line in different dosages. for this, there is a tool called bmdexpress2 that I am using. its input is the normalized counts from RNASeq for each dosage as a big matrix. when it comes to pathway analysis step, unlike hallmarks of ...
pathways rna-seq enrichment written 3 months ago by firatuyulur250
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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 6 months ago by firatuyulur250
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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 7 months ago by firatuyulur250
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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 7 months ago by firatuyulur250
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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 7 months ago by firatuyulur250 • updated 7 months ago by swbarnes24.2k
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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 13 months ago by firatuyulur250

Latest awards to firatuyulur

Scholar 12 weeks ago, created an answer that has been accepted. For A: equal distance between groups in a barplot
Popular Question 5 months ago, created a question with more than 1,000 views. For enhancer RNA counting from RNASeq data
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: Is It Fastq Format

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