User: Noushin N

gravatar for Noushin N
Noushin N370
Reputation:
370
Status:
Trusted
Location:
Baltimore, MD
Scholar ID:
Google Scholar Page
Last seen:
30 minutes ago
Joined:
3 years, 8 months ago
Email:
n**************@gmail.com

Posts by Noushin N

<prev • 75 results • page 1 of 8 • next >
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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 days 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 weeks 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 4 weeks 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 7 weeks 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 7 weeks 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 7 weeks 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 10 weeks 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 10 weeks 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 10 weeks ago by Noushin N370
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Answer: A: Calculating Variant Allele Frequency
... Variant allele frequency in this case refers to the fraction of sequencing reads overlapping a genomic coordinate that support the non-reference (mutant/alternate) allele. Typically, this information is either explicitly listed or readily extractable from VCF files. If not, given that you have the ...
written 10 weeks ago by Noushin N370

Latest awards to Noushin N

Scholar 10 weeks ago, created an answer that has been accepted. For A: Extract allele frequencies from VCF
Scholar 5 months ago, created an answer that has been accepted. For A: Extract allele frequencies from VCF
Popular Question 9 months ago, created a question with more than 1,000 views. For Mutect Allele Counts Vs Mpileup
Popular Question 20 months ago, created a question with more than 1,000 views. For Mutect Allele Counts Vs Mpileup
Popular Question 20 months ago, created a question with more than 1,000 views. For Somatic mutation calling without matched normal
Popular Question 20 months ago, created a question with more than 1,000 views. For Somatic Mutation Phasing
Student 20 months ago, asked a question with at least 3 up-votes. For Somatic mutation calling without matched normal
Popular Question 22 months ago, created a question with more than 1,000 views. For Parsing Base String From Samtools Mpileup
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Parsing Base String From Samtools Mpileup
Supporter 2.9 years ago, voted at least 25 times.

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