User: mforde84

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mforde84320
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Posts by mforde84

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Answer: A: How do I obtain germline mutation for TCGA samples?
... when you look at the available vcf files, there will some that are protected. those will include both somatic and germline calls. so you can intersect with the unprotect somatic calls to get what you want. alternatively you could always use the bam files to generate calls using any number of germlin ...
written 4 days ago by mforde84320
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Comment: C: Why is it absolutely necessary to filter a VCF?
... Ah, fair enough. Methodologically, I think the only suitable way is as Brian says in the comments above. You need a gold standard. Thankfully a lot of time and thought has gone into this problem already, so there are resources readily available for pipeline validation with actual seq data. ...
written 7 days ago by mforde84320
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Comment: C: Finding the Genes corresponding to given SNPs using python
... HOWTO: Annotations using assembly :). But honestly, you'd be surprised how much I see bioinformaticians using python and all they're are doing is making a bunch of system calls. It's both hilarious, and disturbing. I get why someone would want to do this, as I occasionally do it in Rscripts, but st ...
written 7 days ago by mforde84320
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Answer: A: Why is it absolutely necessary to filter a VCF?
... 1) most will be relatively common variants. eg., corresponding ExAC MAF = .4 or even in multiallelic site >.5. one recent data set i was working with 80/100 samples had the same variant, and the corresponding ExAC adj.MAF was approximately .80. 2) most will be synonymous, intergenic, intronic, e ...
written 8 days ago by mforde84320
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Comment: C: Help with linear regression model design
... I figured it out. To do the comparison you would do something like this: makeContrasts(group1 - (group2 + group3) / 2, ....) Thanks again for the help. ...
written 9 days ago by mforde84320
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Comment: C: Help with linear regression model design
... g1 g2 g3 1 0 0 Yes, that is correct. I tried: g1 g2 g3 1 -1 -1 But that gave incorrect results. As you noted before it doesn't sum to 0. ...
written 9 days ago by mforde84320
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Comment: C: Finding the Genes corresponding to given SNPs using python
... If you want to lookup the annotation information for a given dbSNP id, then you need to interface with the dbSNP database directly and do a lookup. Or you can use a variety of web-interface tools available for this purpose, e.g., SNP-nexus takes dbSNP ids as input. If you need to lookup annotation ...
written 9 days ago by mforde84320
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Comment: C: Help with linear regression model design
... I agree that the pairwise test is much more straightforward both in terms of implementation and even interpretation, though my bosses are specifically asking for the contrasts between say g1 - (g2 + g3). I don't think the results will really change but I just do what they tell me to do and report th ...
written 9 days ago by mforde84320
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Comment: C: Help with linear regression model design
... Ah, that makes sense. So essentially I'm just looking at an intercept for each group. One more follow up if you don't mind. In order to capture the combined group contrasts (e.g., between g1 - (g2 + g3)) I've tried creating multiple additional factors which have the appropriate group memberships: ...
written 9 days ago by mforde84320
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Answer: A: Help with linear regression model design
... sorry meant as comment ...
written 9 days ago by mforde84320

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Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Heatmaps: Why and How to use them
Good Answer 15 days ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics in a clinical diagnostic setting versus research (academia)
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