User: igor

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igor4.6k
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Posts by igor

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Comment: C: TAD (Topologically Associating Domain) boundaries
... They are from different cell types. ...
written 3 days ago by igor4.6k
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Comment: C: TAD (Topologically Associating Domain) boundaries
... There should be a description somewhere, but I am not sure where. That would be a question for ENCODE. Regarding bins, most operations in Hi-C are on a bin level since it's not possible to get single-base resolution. This means the genome is broken into bins/regions/windows (usually 10-40 kb). A g ...
written 6 days ago by igor4.6k
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Answer: A: FPKM threshold and filter
... You can try to use a zFPKM transform to define expressed genes: https://bioconductor.org/packages/devel/bioc/vignettes/zFPKM/inst/doc/zFPKM.html > we provide a novel normalization metric, zFPKM, that identifies the > threshold between active and background gene expression; and we show > th ...
written 8 days ago by igor4.6k
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Comment: C: How to deal with PCR artifacts in RNASeq data?
... Can you clarify "looked like a lot of PCR artifacts from the library prep"? Do you mean you have a lot of duplicates or is it something else? Is it just in one group and not the other? ...
written 13 days ago by igor4.6k
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Comment: C: RNA-seq rRNA contamination
... Yes, that is essentially the first method I mentioned. ...
written 13 days ago by igor4.6k
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Answer: A: How to quantify the overlapping reads in paired-end DNA sequencing to check the
... You can calculate the overlap by comparing the read length to the fragment/insert size. There are a few ways to do that. See this previous discussion: https://www.biostars.org/p/65262/ ...
written 13 days ago by igor4.6k
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Comment: C: heatmap using FPKM values
... > the sequencing facility has given me cuffdiff results so that is what > i have to work with If you already have the Cuffdiff results, then you already have differentially expressed genes. ...
written 14 days ago by igor4.6k
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Answer: A: spreadsheet tools alternative
... A lean and simple (only 218 bytes!) spreadsheet app: http://xem.github.io/sheet/ Free, open source, and no extra crud to mess up dates! ...
written 18 days ago by igor4.6k
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Comment: C: spreadsheet tools alternative
... This is not a fair question. You are saying it's too hard to adjust some settings in Excel. Learning how to use a completely new software tool will not be easier. ...
written 18 days ago by igor4.6k
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Answer: A: R package to plot mutational frequency
... I don't know if there is a package for that, but you can use ggplot `geom_jitter` to do something similar. It's not the same, but it will let you see the distribution of the individual values. ![enter image description here][1] [1]: http://ggplot2.tidyverse.org/reference/geom_jitter-4.png ...
written 18 days ago by igor4.6k

Latest awards to igor

Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Best strategy for de novo assembly with illumina reads ?
Popular Question 6 days ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Popular Question 8 days ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Best strategy for de novo assembly with illumina reads ?
Great Question 27 days ago, created a question with more than 5,000 views. For Clustering differences between heatmap.2 and pheatmap
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Popular Question 3 months ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Popular Question 3 months ago, created a question with more than 1,000 views. For Best way to perform single-cell RNA-seq normalization
Student 3 months ago, asked a question with at least 3 up-votes. For ATAC-seq peak calling with MACS
Great Question 3 months ago, created a question with more than 5,000 views. For ATAC-seq peak calling with MACS
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 4 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 5 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Appreciated 5 months ago, created a post with more than 5 votes. For A: read length of sequence
Appreciated 5 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Popular Question 5 months ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis

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