User: firatuyulur

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firatuyulur310
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Posts by firatuyulur

<prev • 47 results • page 1 of 5 • next >
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Comment: C: Bam File: Change Chromosome Notation
... I guess the issue comes with the awk line of the code as it checks the 7th column; being either "=" or "*" and adds "chr" if doesn't match. Then the header lines are also added a "chr" on the 7th column. I don't know about the speed but modifying the awk and tr lines as below could work ``` awk ...
written 4 days ago by firatuyulur310
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Comment: C: genome in IGV session file
... why not load the genome during the session inside IGV and save it as a new session? ...
written 7 months ago by firatuyulur310
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Comment: C: str handling in python
... I don't mind helping although I agree with whats been said. Yet, maybe its me but, I couldn't understand much from what you've typed in. Could you explain a bit better with a full example ...
written 16 months ago by firatuyulur310
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Answer: A: I need allele copy number information for running PyClone
... I used [sequenza][1]. In my case I had both tumour and normal bams. [1]: https://cran.r-project.org/web/packages/sequenza/vignettes/sequenza.html#about ...
written 16 months ago by firatuyulur310
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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 2.6 years ago by firatuyulur310
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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 2.6 years ago by firatuyulur310
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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 2.6 years ago by firatuyulur310
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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 2.6 years ago by firatuyulur310
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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 2.6 years ago by firatuyulur310
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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 2.9 years ago by firatuyulur310

Latest awards to firatuyulur

Popular Question 4 months ago, created a question with more than 1,000 views. For Methylation levels at specific sites
Popular Question 14 months ago, created a question with more than 1,000 views. For Plus and minus strands plotted together
Popular Question 16 months ago, created a question with more than 1,000 views. For multiple SRR in a particular FTP conflict
Popular Question 16 months ago, created a question with more than 1,000 views. For enhancer RNA counting from RNASeq data
Popular Question 21 months ago, created a question with more than 1,000 views. For Plus and minus strands plotted together
Scholar 21 months ago, created an answer that has been accepted. For A: equal distance between groups in a barplot
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Plus and minus strands plotted together
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Plus and minus strands plotted together
Popular Question 2.4 years ago, created a question with more than 1,000 views. For enhancer RNA counting from RNASeq data
Scholar 2.6 years ago, created an answer that has been accepted. For A: equal distance between groups in a barplot
Popular Question 2.8 years ago, created a question with more than 1,000 views. For enhancer RNA counting from RNASeq data
Commentator 4.2 years ago, created a comment with at least 3 up-votes. For C: Is It Fastq Format

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