User: Noushin N

gravatar for Noushin N
Noushin N370
Reputation:
370
Status:
Trusted
Location:
Baltimore, MD
Scholar ID:
Google Scholar Page
Last seen:
1 day ago
Joined:
4 years ago
Email:
n**************@gmail.com

Posts by Noushin N

<prev • 76 results • page 1 of 8 • next >
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Comment: C: B Allele Frequency (VAF) Segmentation Analysis
... If possible, can you show the raw minor allele frequency plot (using scatter plot format of the first figure)? ...
written 3 months ago by Noushin N370
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Comment: C: Where is the BigWig Supplementary Information?
... I checked the supplementary table links on 2 browsers (chrome 56.0 and safari 10.0), and I cannot open them either. ...
written 4 months ago by Noushin N370
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Comment: C: Understanding coverage command
... Probably not the actual reason, but a tempting question here: Can the value of 10 you are reporting possibly be in log2? ...
written 4 months ago by Noushin N370
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Answer: A: is there any R package to measure the efficiency of different exome capture kits
... If you can relax the requirement of being in R, you may want to check out [calculateHsMetrics][1] from Picard. It extracts metrics (including what you mention) from target-capture sequencing experiments and may get the job done. [1]: https://broadinstitute.github.io/picard/picard-metric-definit ...
written 5 months ago by Noushin N370
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Comment: C: How to extract FORMAT information (GT, PG, PI, etc) from each SAMPLE in a vcf fi
... Have you defined your sampleIDs variable before referencing it? Regarding `PG` and `PI` fields, here is a fix that can handle missing values: ``` sample_PG = [record.genotype(sampleID).get('PG') if 'PG' in record.genotype(sampleID) else '.' for sampleID in sampleIDs] sample_PI = [record.genotype( ...
written 5 months ago by Noushin N370
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Comment: C: How to extract FORMAT information (GT, PG, PI, etc) from each SAMPLE in a vcf fi
... Thanks for the tip! I wasn't aware that this syntax is discouraged. ...
written 5 months ago by Noushin N370
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Answer: A: How to extract FORMAT information (GT, PG, PI, etc) from each SAMPLE in a vcf fi
... ### Problem 1 It can be addressed by using python list comprehensions as follows: If you are sure that all samples include `GT` field, you can use: ``` sample_genotypes = [record.genotype(sampleID)['GT'] for sampleID in sampleIDs] ``` ``` print >>output, '\t'.join([contig, pos, ref_allele, ...
written 5 months ago by Noushin N370
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Answer: A: Benjamin Hochberg adjust P-values
... I would like to add a cautionary note about the above answer here, regarding the [nonmonotonocity][1] of q-values (corrected p-values) that would result from the formula. The source code for the p.adjust function in R is here: > BH = { > i <- lp:1L > o <- order( ...
written 6 months ago by Noushin N370
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Comment: C: Calculating Variant Allele Frequency
... By that I mean that in the germline (normal cell), the individual has two copies of the reference allele. By mentioning this, I am trying to exclude cases where the germline is heterozygous, and one the reference allele is lost by somatic copy number events (LOH). ...
written 6 months ago by Noushin N370
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Comment: C: Calculating Variant Allele Frequency
... The referenced scripts parses allele counts from an mpileup format file. From the VCF snippet you attached, in the header you can see: > ##INFO= > ##INFO= > ##INFO= The variant allele frequency (assuming that the germline is homozygous reference) is VAF = AD / DP = Depth of A ...
written 6 months ago by Noushin N370

Latest awards to Noushin N

Scholar 6 months ago, created an answer that has been accepted. For A: Extract allele frequencies from VCF
Scholar 9 months ago, created an answer that has been accepted. For A: Extract allele frequencies from VCF
Popular Question 12 months ago, created a question with more than 1,000 views. For Mutect Allele Counts Vs Mpileup
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Mutect Allele Counts Vs Mpileup
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Somatic mutation calling without matched normal
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Somatic Mutation Phasing
Student 2.0 years ago, asked a question with at least 3 up-votes. For Somatic mutation calling without matched normal
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Parsing Base String From Samtools Mpileup
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Parsing Base String From Samtools Mpileup
Supporter 3.2 years ago, voted at least 25 times.

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