User: igor

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igor4.9k
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Posts by igor

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Answer: A: mitichondrial marker genes in SCRNAseq
... Based on the code, they are just searching for genes that start with "MT-". Alternatively, you can search for search for genes on "chrM" in your GTF. ...
written 2 minutes ago by igor4.9k
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Comment: C: edgeR analysis dilemma -- what samples to include
... I agree with your options. However, it really depends on your question. For example, you can plot significant genes from C vs A for all samples to see how B samples cluster. Are they more similar to C or A? ...
written 2 days ago by igor4.9k
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Answer: A: How to screen for rRNA and gDNA contamination in RNA-seq data?
... For gDNA, you already have your answer to some degree. As you mentioned, 20-80% of your reads are assigned to "no feature". In other words, they are not overlapping exons, so they are intronic/intergenic. You can blame that on poor annotation. However, the samples should be consistent. If one is 20% ...
written 2 days ago by igor4.9k
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Answer: A: edgeR analysis dilemma -- what samples to include
... Regardless of statistics, only option 2 is realistic. Eventually someone is going to ask you to: - compare conditions A and B - put gene X for all conditions on the same bar plot (need to be normalized together) - add significance levels for each comparison (all pairwise comparison combinations ...
written 3 days ago by igor4.9k
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Answer: A: How to mark significance in R-making boxplot
... Based on your `boxplot()` code, your columns of interest are `NN` and `C`. You should be using those for `ggboxplot()`. You are using `CR` and `CN`. ...
written 7 days ago by igor4.9k
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Comment: C: what is the best way to extract specific region of a RNA seq
... IGV is for visualization. If you would like to correlate with methylation, you need extract the expression values. In other words, do a proper RNA-seq analysis. Essentially, that means calculating the raw counts for the genes and then normalizing them across your samples. ...
written 8 days ago by igor4.9k
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Comment: C: what is the best way to extract specific region of a RNA seq
... You should be okay with the defaults. Then you can change the parameters based on how it looks. ...
written 12 days ago by igor4.9k
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Comment: C: Strategies to call variants from a cancer sample
... I would say somatic and germline variants are completely different analysis, so you can't really combine them. For germline, you can call them in the N and use T as the validation sample. TCGA PDAC is a nice paper where they discuss a lot of somatic and germline variants side by side: https://www. ...
written 13 days ago by igor4.9k
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Comment: C: Differential expression of scRNA-seq after Seurat
... I didn't realize your samples were in separate objects. You can merge multiple Seurat objects into a single Seurat object. All the annotations in the `meta.data` slot should be preserved. ...
written 13 days ago by igor4.9k
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Answer: A: CNA vs mRNA Expression level
... Check this previous discussion on this topic: https://www.biostars.org/p/274762/ ...
written 13 days ago by igor4.9k

Latest awards to igor

Good Answer 8 days ago, created an answer that was upvoted at least 5 times. For A: read length of sequence
Popular Question 12 days ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Scholar 12 days ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Appreciated 15 days ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Popular Question 18 days ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Scholar 26 days ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Best strategy for de novo assembly with illumina reads ?
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Best strategy for de novo assembly with illumina reads ?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Great Question 11 weeks ago, created a question with more than 5,000 views. For Clustering differences between heatmap.2 and pheatmap
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Popular Question 5 months ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Popular Question 5 months ago, created a question with more than 1,000 views. For Best way to perform single-cell RNA-seq normalization
Student 5 months ago, asked a question with at least 3 up-votes. For ATAC-seq peak calling with MACS
Great Question 5 months ago, created a question with more than 5,000 views. For ATAC-seq peak calling with MACS
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 6 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)

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