Moderator: Brian Bushnell

gravatar for Brian Bushnell
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Walnut Creek, USA
Website:
http://sourceforge.net...
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2 years, 6 months ago
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I like to program in Java.

Posts by Brian Bushnell

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Comment: C: What does BAF mean?
... Ah, that makes sense. Thanks! ...
written 1 day ago by Brian Bushnell11k
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What does BAF mean?
... I recently encountered the term "BAF" in a post on Biostars. I've looked up the definition, which is "B-Allele Frequency" (the extended definition is no more enlightening; one allele is A and the other is B). To me, that has no meaning other than being "Allele Frequency" with perhaps implicit assu ...
variant-calling baf written 1 day ago by Brian Bushnell11k • updated 1 day ago by Devon Ryan66k
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Comment: C: Are there NGS-based CNV callers that utilise allele frequency?
... Thanks for the reply. That still seems very vague, though. According to what you said, the definition I posted is wrong as there is an implicit "B is not the reference allele". Does anyone have a better definition of BAF? ...
written 1 day ago by Brian Bushnell11k
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Comment: C: Are there NGS-based CNV callers that utilise allele frequency?
... I had to look up BAF. Where did that come from? What's wrong with "AF"? I got: > The B-Allele Frequency is a normalized measure of the allelic > intensity ratio of two alleles (A and B), such that a BAF of 1 or 0 > indicates the complete absence of one of the two alleles (e.g. AA or > ...
written 1 day ago by Brian Bushnell11k
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Comment: C: From bam paired files to fasta
... > So basically with whole genome data assembled by reference mapping, > pulling out protein coding genes or mRNA is complicated assignment? Yes, that's extremely complicated :) There's no perfect solution for it. But it seems likely that Istvan's recommendation of FastaAlternateReferenceMak ...
written 1 day ago by Brian Bushnell11k
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Answer: A: Bowtie2/HISAT using single-end to generate FPKM???
... FPKM does not require paired-end reads. For single-ended reads, it makes the calculation much simpler since you never have the problem of the two ends mapping to different genes :) It would be helpful if you could post the first... 16 lines of the file rather than the first 4 lines, to see if mayb ...
written 1 day ago by Brian Bushnell11k
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Comment: C: Are these false somatic variants? Visual inspection with IGV
... I don't understand why you think they are false. Can you explain? I mean, if they are in the tumor but not normal I would say it is definitely real (of course it could be an imperfect replication, but I don't see that as particularly being less real). If they are in both, I'd say it might be real ...
written 1 day ago by Brian Bushnell11k
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Comment: C: Are these false somatic variants? Visual inspection with IGV
... > Depending on the flanking sequence there may be a more parsimonious > explanation. For example, in some sequencing contexts, the 3 SNVs > could be explained by 1bp insertion that the aligner prefers to align > as 3 SNVs. Are the reads containing the variants soft clipped? I think that ...
written 1 day ago by Brian Bushnell11k
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Comment: C: In GWAS Studies, how to understand "97 SNPs explain 2.7% of BMI"?
... That probably means something like... "You can determine someone's racial composition or location by looking at their SNPs. Those are both factors in BMI, which makes the SNPs correlated. These SNPs have no known causal relationship with BMI, but it's easy to use them to publish papers." ...
written 2 days ago by Brian Bushnell11k
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Answer: A: What Are The Open Source Alternatives To Gatk?
... GATK is a pretty big toolset, so it's hard to replace all of it in one fell swoop. But as far as variant-calling goes, you can use BBMap's "callvariants.sh" to get better results (from my tests) in a tiny fraction of the time. The BBMap package is fully open-source. It's also easy to use - "callv ...
written 3 days ago by Brian Bushnell11k

Latest awards to Brian Bushnell

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
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Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Commentator 10 days ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Scholar 12 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
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Scholar 19 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
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Teacher 26 days ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
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Scholar 4 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Scholar 4 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
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Scholar 4 weeks ago, created an answer that has been accepted. For A: How to download human whole genome database?
Scholar 4 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Scholar 7 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
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Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming

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