User: firatuyulur

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firatuyulur260
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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 9 months ago by firatuyulur260
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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 9 months ago by firatuyulur260
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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 9 months ago by firatuyulur260
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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 9 months ago by firatuyulur260
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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 9 months ago by firatuyulur260
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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 13 months ago by firatuyulur260
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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 13 months ago by firatuyulur260
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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 13 months ago by firatuyulur260
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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 13 months ago by firatuyulur260 • updated 13 months ago by swbarnes25.2k
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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 19 months ago by firatuyulur260

Latest awards to firatuyulur

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Plus and minus strands plotted together
Popular Question 6 months ago, created a question with more than 1,000 views. For enhancer RNA counting from RNASeq data
Scholar 9 months ago, created an answer that has been accepted. For A: equal distance between groups in a barplot
Popular Question 11 months ago, created a question with more than 1,000 views. For enhancer RNA counting from RNASeq data
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Is It Fastq Format

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