User: AcademicDialysis

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Posts by AcademicDialysis

<prev • 7 results • page 1 of 1 • next >
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Answer: A: How to compare a tumour sample to multiple normal samples in Freebayes
... I believe you mean to **filter in somatic** SNPs and **filter out germline** SNPs. Using multiple normal samples is often known as a pool or panel of normals. More [about that here][1]. I looked around a bit at Freebayes and couldn't find anything directly from them. Looks like bcbio [supports poole ...
written 2.3 years ago by AcademicDialysis70
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Comment: A: Varscan: Variant Detection In Massively Parallel Sequencing Data
... Does VarScan2 work for somatic mutation calling against pooled normal samples? I see that it works for germline calling against a pool of normals, and somatic calling against matched-normal data. Is there a way I can "hack" either method? Thanks! ...
written 2.3 years ago by AcademicDialysis70
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Comment: A: How do I call somatic indels from a VCF file?
... **Update:** You can see Andy Rimmer's answer to this question on the Google Group for Platypus here: https://groups.google.com/forum/#!topic/platypus-users/1kIfOBDfkfA ...
written 2.3 years ago by AcademicDialysis70
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Answer: A: Hera: A new tool for RNA-Seq analysis
... Neat! There must be some witchcraft under the hood for it to be doing all those functions in a third of the time or less as the current industry standards. Can it handle matched-normal datasets, or running a tumor sample against a panel of normals? Also, do you have data other than speed that would ...
written 2.3 years ago by AcademicDialysis70
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How do I call somatic indels from a VCF file?
... Hi, I'm doing an analysis to find Indels in a cancer sample. I've used [Platypus][1] to call variants and VCF tools to filter out all variations except indels. I have matched normal exome data, and [the recommendation][2] is to call the indels on both the tumor and normal sample at the same time ag ...
vcf indel mutation platypus cancer written 2.3 years ago by AcademicDialysis70
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Comment: C: How can I use BLAST to extract chloroplast sequences from DNA reads?
... Since the closest reference is just in the same family, I don't think my consensus sequences would be very large. Should I just blast and then use those reads to do de novo assembly? Or should I still use bwa and just use all of those sequences as reference?   Thanks! ...
written 4.6 years ago by AcademicDialysis70
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How can I use BLAST to extract chloroplast sequences from DNA reads?
... I'm trying to extract the chloroplast sequences from my reads, as Whole Genome Sequencing was used to produce them. This paper: http://www.sciencedirect.com/science/article/pii/S2214540013000169 mentions that to do this, they BLASTed their reads against all of the known genomes in the same family. ...
chloroplast database alignment blast written 4.6 years ago by AcademicDialysis70 • updated 4.6 years ago by 5heikki8.6k

Latest awards to AcademicDialysis

Appreciated 2.3 years ago, created a post with more than 5 votes. For A: Hera: A new tool for RNA-Seq analysis
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Hera: A new tool for RNA-Seq analysis
Popular Question 4.5 years ago, created a question with more than 1,000 views. For How can I use BLAST to extract chloroplast sequences from DNA reads?

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