User: igor

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igor5.2k
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Posts by igor

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Comment: C: 1D^2: Oxford nanopre technology
... They've had 2D for a long time. By the time you got to FASTQs, it was indistinguishable from 1D (unless you specifically split template and complement strands). I assume the output would be similar for 1D^2. ...
written 17 hours ago by igor5.2k
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Comment: C: how to find a particular GEO dataset or cohort in cBioportal and TCGA
... > what I want to know is how can I find what datasets are part of those > 11 and 22 datasets? If I am not wrong some of them, if not all, must > be part of GEO. TCGA data is not in GEO. > why is there difference between number of datasets in GDC TCGA > Prostate Cancer (PRAD) and coh ...
written 5 days ago by igor5.2k
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Comment: C: MuTect2 still discard many reads, how to fix?
... If you don't know, then you should probably not retain. There is a reason why they are not retained by default. You can consult GATK Best Practices for more info: https://software.broadinstitute.org/gatk/best-practices/workflow?id=11146 ...
written 5 days ago by igor5.2k
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Comment: C: Gene expression units explained: RPM, RPKM, FPKM and TPM
... I am not sure I understand. You can't adjust transcripts. They are already defined. ...
written 11 days ago by igor5.2k
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Answer: A: Reads aligning in unstranded RNA-Seq library
... STAR aligns to the genome. The genome FASTA is technically only one strand. The strand info is based on whether the read is identical sequence as the FASTA or the reverse complement. For example, two reads `AAAT` and `TTTA` would align to the same place, but in different orientations. Thus, they ar ...
written 13 days ago by igor5.2k
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Answer: A: trying to use DESeq2, how to set up the data files
... If you are a non-programmer, it might be easier to just use something like https://gallery.shinyapps.io/DEApp/ . It uses DESeq2 on the backend and has a nice tutorial. ...
written 22 days ago by igor5.2k
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Answer: A: How do I subset gene loci with no difference from DeSeq2 output?
... If you are using padj<0.1 as significant, then the rest are not significant. Of course, not significant could be both not altered and without sufficient information to make the call. Regarding NAs, that is actually described in the [vignette][1]: > If within a row, all samples have zero coun ...
written 22 days ago by igor5.2k
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Answer: A: minION from oxford nanopore, is it still so promising?
... From limited personal experience, each new flow cell is a significant improvement over the previous generation. If you last used Nanopore more than a year ago, you will be surprised by the difference. I just saw a good [blog post][1] on this topic (as it relates to PacBio, which is really the most ...
written 28 days ago by igor5.2k
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Answer: A: Data Visualization Web App
... If you want to make a Python-based visualization app, you are probably looking for Dash: https://plot.ly/products/dash/ > Dash is a Python framework for building analytical web applications. > No JavaScript required. ...
written 4 weeks ago by igor5.2k
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Answer: A: pathway for single cell RNA-seq
... If you only take the top 50 genes, you might be missing a lot of information. Also, depending on what the other clusters are, the differentially expressed genes will change. You can take the average expression of all genes for each cluster and then use a cell type deconvolution tool. Check this prev ...
written 4 weeks ago by igor5.2k

Latest awards to igor

Popular Question 8 days ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Commentator 13 days ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 21 days ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Popular Question 23 days ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Scholar 6 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 Why are there multiple GFP nucleotide sequences?
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Best way to perform single-cell RNA-seq normalization
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: read length of sequence
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
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: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Teacher 3 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: Best strategy for de novo assembly with illumina reads ?
Popular Question 4 months ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Best strategy for de novo assembly with illumina reads ?
Popular Question 4 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)
Great Question 5 months ago, created a question with more than 5,000 views. For Clustering differences between heatmap.2 and pheatmap
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis

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