Moderator: karl.stamm

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karl.stamm3.3k
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Posts by karl.stamm

<prev • 434 results • page 1 of 44 • next >
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Comment: C: STAR alignment killed
... And maybe that --runThreadN=10 is multiplying the requirements. Try 1 thread, and monitor memory usage, then try two threads and monitor memory usage. ...
written 10 days ago by karl.stamm3.3k
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Answer: A: BWA mem of a heavily masked reference index takes more time than the normal refe
... The masking doesnt make the reference genome smaller, it's the same basepair length. What masking does however is let your reads possibly align in many more places. Every masked section could be a match to either end of your read. So rather than using BWA's intelligent "seed" technique to limit al ...
written 5 weeks ago by karl.stamm3.3k
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Comment: C: DESeq2 Error while applying standard analysis
... It says WARNING the design is ~ 1 (just an intercept). is this intended?** ...
written 5 weeks ago by karl.stamm3.3k
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Comment: C: Subsampling procedure for differential analysis
... Theyre both true in different ways. "The LFC is >6" ...
written 6 weeks ago by karl.stamm3.3k
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Comment: C: Subsampling procedure for differential analysis
... Yes of course increasing FDR cutoff from 0.05 to 0.50 will give you lots more differentially expressed genes. I think the random sub-sampling is going to give uninterpretable results. Maybe try hold-one-out, where you run 29 vs 3 with each sample held out, creating 30 different result sets, and se ...
written 6 weeks ago by karl.stamm3.3k
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Comment: C: Subsampling procedure for differential analysis
... Looks like your tumor samples are widely different from each other. So the result of just two genes is correct. Those are the two that are consistently different between the normal/tumor condition. Any other genes may not be distinct in some group of your tumor samples. ...
written 6 weeks ago by karl.stamm3.3k
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Comment: C: Rarefaction on R
... Okay maybe a Venn Diagram can show how many things are shared or unique between sets. But you have 17 groups, so that's a terrible mess. If it was 2-3 groups this could be a good visualization. With 17 groups, do you have any kind of experimental hypothesis? "Showing how diverse" could just be a ...
written 11 weeks ago by karl.stamm3.3k
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Comment: C: Rarefaction on R
... samples of what? A sample, to me is a tube of serum, how do you get more species than samples? what do you need from "test for richness" ? Sounds quite rich. ...
written 11 weeks ago by karl.stamm3.3k
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Comment: C: How representative the solid tumor sample is to that entire tumor lesion in term
... No, somatic mutations happen in individual cells, so you'll start with one cell with an arbitrary background, who suddenly evolves the ability to multiply quickly. It can become the majority of tumor mass. Its offspring may continue to mutate, or may stably reproduce the original. I think the firs ...
written 5 months ago by karl.stamm3.3k
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Comment: C: How representative the solid tumor sample is to that entire tumor lesion in term
... It's going to vary by tumor type. Fast growers will be homogeneous due to "clonality" but there's no measure of "the entire lesion". ...
written 5 months ago by karl.stamm3.3k

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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Popular Question 4 months ago, created a question with more than 1,000 views. For Can I run VEP on a VCF twice?
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
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Appreciated 11 months ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
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Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
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Scholar 2.4 years ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Appreciated 2.4 years ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
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Scholar 2.7 years ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?

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