User: maheetha.b

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maheetha.b60
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Posts by maheetha.b

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Cancer Patient Derived Xenograft (PDX) Genomic Analysis
... Hi! I'm interested in doing this as well. Has anyone actually tested Xenome vs. Disambiguate vs. aligning to mouse+human reference? ...
written 12 months ago by maheetha.b60
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Comment: A: BWA-MEM output for two species
... I'm working with mice and human. I know many genes are similar, 80% 1-1 correlation, but not sure how much of it is in coding regions. I'll take a look! thank you! But again, I feel like there is no way to differentiate between reads that map equally well to both species (although highly unlikely s ...
written 15 months ago by maheetha.b60
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BWA-MEM output for two species
... Hello. I have a fastq file that contains targeted panel DNA from two species. The current methodology is to map it to a combined reference genome. I know that BWA-MEM gives a mapping quality 0 for for reads that have been mapped to multiple places, and if it's 2 locations, the MAPQ score is 3. ...
bwamem disambiguate written 15 months ago by maheetha.b60
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Comment: A: Explain the definition of DELLY output
... Thank you for the responses. This has been helpful. ...
written 15 months ago by maheetha.b60
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Comment: C: Structural Variant annotation
... I appreciate that it should have been detailed, but I was wondering if there was something for structural variants in general outside of DELLY. ...
written 15 months ago by maheetha.b60
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Comment: C: Structural Variant annotation
... Thank you for the comments. Papers are papers. They're geared towards audiences that already know the ins and outs of structural variants. I understand what a VCF/BCF format is, but my annotation has columns named split read support and tumor split read support and tumor variant allele count, and ...
written 15 months ago by maheetha.b60
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Explain the definition of DELLY output
... I'm looking at a DELLY annotated file, I am having some difficulty visualizing the difference between PairEndReadSupport, SplitReadSupport, TumorVariantCount, TumorSplitVariantCount, TumorReadCount. Can someone familiar with DELLY output explain the differences between these? I assume that Paire ...
delly written 15 months ago by maheetha.b60
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Structural Variant annotation
... Hello, I'm trying to understand how structural variants are reported from tools, and then subsequently how they're annotated in MAF format (if at all). Can someone point me to a papers or tutorials? ...
structural variants delly written 15 months ago by maheetha.b60 • updated 15 months ago by d-cameron1.9k
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Comment: C: germline vs. somatic mutations in cancer samples
... This was an amazing explanation. This all makes sense. I just needed to clarify that you'd never see a "somatic mutation" in a blood cell (non cancerous) that was large enough for a germline-variant caller to call it. Thank you! ...
written 19 months ago by maheetha.b60
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germline vs. somatic mutations in cancer samples
... So when researchers talking about their sequencing projects, some of them are taking blood samples from cancer patients who don't have blood cancer. I understand that because blood cells are not cancerous, they would not show somatic mutations associated with the tumor. But this does not necessari ...
somatic whole exome sequencing germline written 19 months ago by maheetha.b60 • updated 19 months ago by Dan Gaston7.1k

Latest awards to maheetha.b

Popular Question 7 months ago, created a question with more than 1,000 views. For unmapped reads from Tophat
Popular Question 11 months ago, created a question with more than 1,000 views. For germline vs. somatic mutations in cancer samples
Student 19 months ago, asked a question with at least 3 up-votes. For germline vs. somatic mutations in cancer samples

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