User: Sam

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Sam30
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12 hours ago
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1 year, 4 months ago
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Posts by Sam

<prev • 44 results • page 1 of 5 • next >
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Comment: C: separating dataset by a specific character
... Why not convert the bed file to a more suitable format using linux? Something like cat datahg38.bed | tr "\:" "\t" | tr "-" "\t" > datahg38_format.bed ...
written 14 hours ago by Sam30
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Comment: C: How to avoid overfitting using SVA?
... To me personally it seems that once we perform SVA, we introduce an unverified assumption to the analysis. The assumption of the surrogate variables that we estimated and removed is ultimately unverifiable. So once SVA is performed, it becomes mandatory to validate the results of the analysis using ...
written 23 hours ago by Sam30
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How to avoid overfitting using SVA?
... The sva package enables estimation of surrogate variables from the data itself, so that unwanted sources of variation can be removed. How can one make sure that he does not remove too much variation? What are general guidelines? ...
sva rna-seq written 23 hours ago by Sam30
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Comment: C: RNA-SEQ where only a subset of genes is of interest
... Biological criteria, not statistical criteria. This is the pathway(s) of most interest to the PI in the first place. ...
written 8 days ago by Sam30
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RNA-SEQ where only a subset of genes is of interest
... I am performing an analysis on RNA-Seq data, where only genes relating to specific pathways are of interest to the researcher. 1) One option is normalizing, estimating the dispersion and performing DE with DESeq2 *as usual* (since DESeq's assumption that most genes are not differentially expressed ...
deseq rna-seq written 8 days ago by Sam30 • updated 8 days ago by swbarnes28.6k
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Comment: C: generate .tab file for snippy with filenames & paths
... See detailed discussion at https://stackoverflow.com/questions/1251999/how-can-i-replace-a-newline-n-using-sed ...
written 8 days ago by Sam30
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Answer: A: Tophat alignment and -g parameter
... Simon Andrews writes [here][1] > if you run tophat with -g1 then all of the hits reported are given a > mapping quality of 50, even if there are multiple perfect hits with > the same strength in the file. It looks like tophat is calculating > the mapq score after the output filtering ...
written 13 days ago by Sam30
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Comment: C: Tophat alignment and -g parameter
... Thanks. I would still love to get an answer, if it is known. ...
written 13 days ago by Sam30
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Tophat alignment and -g parameter
... An alignment I was running of 150 bp paired-end data took a lot of time (more than a week) to run. As the stage that took it too much time in the log file was "reporting output tracks" , I thought to limit the *output* of tophat via "-g 1" (--max-multihits), thinking this is the reporting of all com ...
tophat rna-seq written 13 days ago by Sam30
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Answer: A: Htseq unable to process last read
... Turns out that the specific parameter which causes this problem is -o Samp1_w_feature_PE.bam -p bam Counting paired-end reads AND creating the output in bam format causes an error. None of them separately causes an error. I was able to output bam, when counting single reads, and more importa ...
written 17 days ago by Sam30

Latest awards to Sam

Scholar 17 days ago, created an answer that has been accepted. For A: What is the right way to convert probe names from Brainarray Custom CDF to Ensem
Scholar 3 months ago, created an answer that has been accepted. For A: What is the right way to convert probe names from Brainarray Custom CDF to Ensem

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