User: igor

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igor3.4k
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Posts by igor

<prev • 619 results • page 1 of 62 • next >
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Comment: C: gnu parallel for RNA seq
... Why do you need to use `parallel` specifically? Just send them to background with `&` at the end of the command. Much easier in my opinion if you are not familiar with `parallel`. http://hacktux.com/bash/ampersand ...
written 24 minutes ago by igor3.4k
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Answer: A: How do I get the weights of genes used in PCA in DESeq2?
... The `plotPCA` function performs PCA like this: plotPCA.DESeqTransform = function(object, intgroup="condition", ntop=500, returnData=FALSE) { # calculate the variance for each gene rv <- rowVars(assay(object)) # select the ntop genes by variance select <- o ...
written 31 minutes ago by igor3.4k
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Comment: C: Difference between 'bedgraph' and 'bw' files
... Yes. See IGV docs: http://software.broadinstitute.org/software/igv/FileFormats ...
written 42 minutes ago by igor3.4k
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Answer: A: Difference between 'bedgraph' and 'bw' files
... BedGraph definition: https://genome.ucsc.edu/goldenpath/help/bedgraph.html BigWig (bw) definition: https://genome.ucsc.edu/goldenpath/help/bigWig.html Comparison of track formats: http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format ...
written 44 minutes ago by igor3.4k
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Comment: C: RNA-seq enrichment analysis with only one sample
... As it says in that post: > When comparing transcript concentrations in two samples on an array, > all one can really say is that the transcript is enriched in one > relative to the other. Whether up-regulation or down regulation is > going on, is a hypothesis for further exploration in ...
written 48 minutes ago by igor3.4k
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Comment: C: RNA-seq enrichment analysis with only one sample
... Where did it say that using up/down regulation is a misconception? In your case, that would actually not be possible since you only have one group, so you might be misinterpreting that. ...
written 21 hours ago by igor3.4k
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Answer: A: Cuffdiff showing 5k significat genes
... The number of significant genes can vary widely depending on many factors. Without knowing anything about your experiment, it's impossible for someone to say what is a reasonable amount. If you think you are getting too many genes, change the significance threshold. The cutoff is mostly arbitrary. ...
written 21 hours ago by igor3.4k
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Comment: C: 10x Supernova de novo assembly
... No. It was a different species. Should be around 0.8 Gb. So does it mean half the genome was missing for you? Is that normal? ...
written 1 day ago by igor3.4k
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Comment: C: 10x Supernova de novo assembly
... In case anyone is wondering, my Supernova run finally finished. It took 6 weeks. Obviously something is wrong since the output is essentially useless (0.02 Gb assembly size), but at least I don't have to wonder anymore. This is the summary report: ----------------------------------------------- ...
written 2 days ago by igor3.4k
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Comment: C: Visualize Mutation Frequency
... Yes, it's going to be hard to do this without any programming. Some of these have nice tutorials, so you might be able to follow them if you know some basic R. ...
written 3 days ago by igor3.4k

Latest awards to igor

Teacher 5 days ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 5 days ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Student 11 days ago, asked a question with at least 3 up-votes. For Using PhiX to estimate bisulfite conversion rate
Scholar 12 days ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Best way to perform single-cell RNA-seq normalization
Scholar 7 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Good Question 10 weeks ago, asked a question that was upvoted at least 5 times. For ATAC-seq peak calling with MACS
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: read length of sequence
Scholar 12 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Popular Question 3 months ago, created a question with more than 1,000 views. For Faster BLAST alternative
Popular Question 3 months ago, created a question with more than 1,000 views. For Faster BLAST alternative
Appreciated 3 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
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?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Student 5 months ago, asked a question with at least 3 up-votes. For Using PhiX to estimate bisulfite conversion rate
Scholar 5 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Scholar 5 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Scholar 5 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data

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