User: igor

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igor3.1k
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Posts by igor

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Comment: C: nucleosome positioning using ATAC-seq
... I think when they say nucleosome-seq, they mean something like MNase-seq where all reads are capturing the nucleosomes. ...
written 4 days ago by igor3.1k
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Comment: C: nucleosome positioning using ATAC-seq
... MACS is for peak calling. For ATAC-seq, that would be open chromatin. Nucleosome positioning is something else. Figure 1 here is helpful: https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/1756-8935-7-33 ...
written 5 days ago by igor3.1k
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Comment: C: How to convert bedgraph to bigwig?
... Try running `./bedGraphToBigWig` (in current directory), not `bedGraphToBigWig` (searches $PATH). You may also need to make it executable (`chmod a+x ./bedGraphToBigWig`) ...
written 5 days ago by igor3.1k
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Comment: C: Why is TCGA Genomic Data Commons missing some data?
... Apparently I was wrong about that. Got a nice response quickly: > There was a problem during the initial import of TCGA data that > resulted in some of the TCGA-LAML being missed. Our development team > is currently working on fixing this issue, but I'm not sure when it > will be resol ...
written 5 days ago by igor3.1k
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Answer: A: RNA contamination in WGS data
... Considering how unstable RNA is, I think it would be difficult to get RNA contamination. If you just want to spot-check, you can look at the coverage tracks for highly-expressed housekeeping genes. If there is RNA contamination, you should see higher coverage at the exons. WGS coverage should be fa ...
written 5 days ago by igor3.1k
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Comment: C: Why is TCGA Genomic Data Commons missing some data?
... I haven't yet. Was hoping this would be faster and provide an unbiased answer. ...
written 5 days ago by igor3.1k
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Comment: C: RNAseq read depth
... For HiSeq, PE100 should only be about twice the cost of SE50. If you are getting charged 3X for PE75 over SE50, you should ask about that. Also, that's just for sequencing. The libraries are going to be the same price and those are a significant portion of the total cost. You can definitely afford ...
written 5 days ago by igor3.1k
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Why is TCGA Genomic Data Commons missing some data?
... Last summer, TCGA data moved from TCGA Data Portal to the Genomic Data Commons. However, for some reason, some data is missing. At first, I thought it was a temporary glitch, but this hasn't changed over time. For example, at [GDAC Firebrowse][1], there are 194 TCGA-LAML 450K samples (2016-01-28 b ...
tcga written 5 days ago by igor3.1k
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Comment: C: How to convert bedgraph to bigwig?
... There should not be any installation. You just download the binary and run it. ...
written 5 days ago by igor3.1k
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nucleosome positioning using ATAC-seq
... Are there any tools for nucleosome positioning using ATAC-seq data? I am aware of NucleoATAC, but that is the only I found. The original ATAC-seq paper used Danpos, which is designed for MNase-seq, and they even mention it may not be ideal. That may not be a good alternative. ...
nucleosome atac-seq written 5 days ago by igor3.1k • updated 5 days ago by ejm32150

Latest awards to igor

Popular Question 17 days ago, created a question with more than 1,000 views. For Best way to perform single-cell RNA-seq normalization
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Scholar 22 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: How detrimental are duplicate reads in RNAseq experiments?
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Good Question 5 weeks ago, asked a question that was upvoted at least 5 times. For ATAC-seq peak calling with MACS
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: read length of sequence
Scholar 8 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Faster BLAST alternative
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Faster BLAST alternative
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Scholar 3 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Student 3 months ago, asked a question with at least 3 up-votes. For Using PhiX to estimate bisulfite conversion rate
Scholar 4 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
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: How detrimental are duplicate reads in RNAseq experiments?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Scholar 4 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: read length of sequence
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Scholar 4 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data

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