User: Noushin N

gravatar for Noushin N
Noushin N530
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530
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Location:
Baltimore, MD
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Last seen:
3 days, 15 hours ago
Joined:
5 years, 8 months ago
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Posts by Noushin N

<prev • 86 results • page 1 of 9 • next >
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Intra-tumor Heterogeneity / Mutation Cellular Fraction in TCGA Data
... Hello, I was wondering if anyone is aware of an online resource where information on mutation cancer cell fraction estimates for TCGA samples can be retrieved. I am aware of two excellent studies which have performed the exact analysis to derive the above. But I cannot locate the corresponding va ...
heterogeneity tcga written 4 weeks ago by Noushin N530
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Comment: A: How to find patient sample.type in TCGA-PRAD ?
... You can make a table that translates the numeric code to the sample types listed [here][1]. [1]: https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes ...
written 8 months ago by Noushin N530
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Answer: A: Inconsistency of allele depth in BAM and VCF
... You are right about the likely reason of this discrepancy. Essentially, you have to compare the filters used in the utility you are using for bam review (e.g. samtools) and the variant caller. A few choices are: - duplicate read exclusion - read mapping quality score filter - read passing qual ...
written 9 months ago by Noushin N530
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Comment: C: Why GWASs cannot speculate what kind of mutation the SNP would cause?
... Great point! Thanks for the addition, Collin! ...
written 12 months ago by Noushin N530
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Answer: A: identifying TP53 germline mutations which are also in tumor cells.
... You are likely able to do this in a more straightforward manner as follows: 1. Identify all the germline TP53 variants in the normal sample 2. Inspect the tumor sample at those positions using `samtools mpileup` Normally, one expects to see germline variants in tumor sample as well; Even in case ...
written 12 months ago by Noushin N530
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Answer: A: Is it possible to check whether a sample is progeny of the other two samples fro
... I do not know if there are established tools for this purpose; but I think one should be answer this relatively easily given the data you mentioned. Assuming that you are looking at human genomes, you can compare the genotypes across a set of common polymorphisms (e.g. common SNPs from dbSNP). If ...
written 12 months ago by Noushin N530
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Answer: A: Why GWASs cannot speculate what kind of mutation the SNP would cause?
... Adding to the response by swbarnes2, many of the variants identified in GWAS are located in non-coding regions of the genome and will function not by altering the protein coding sequences, but by regulation of gene expression. ...
written 12 months ago by Noushin N530
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Answer: A: Changing Chromosome Notation in Bam Files to Include Sample ID
... This doesn't sound like a good idea. I realize that you mention the reads have already been re-aligned to a common reference; but alignment is typically just the first step in the analysis pipeline. Re-naming chromosomes to non-standard ones will likely result in error and/or inaccuracy in many down ...
written 12 months ago by Noushin N530
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Answer: A: Remove columns and rows which have only NAs without deleting all the data
... Assuming that you want to remove any rows or columns containing `NA` values, you can try the following approach. x = matrix(seq(49), ncol = 7) x[2,5]= NA x [,1] [,2] [,3] [,4] [,5] [,6] [,7] [1,] 1 8 15 22 29 36 43 [2,] 2 9 16 23 NA 37 ...
written 19 months ago by Noushin N530
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Answer: A: retrieve genomic coordinate on mRNA
... [Transvar webserver][1] can handle this task. As you said, there will likely be multiple hits for each genomic positions. [1]: http://bioinformatics.mdanderson.org/transvarweb/ ...
written 20 months ago by Noushin N530

Latest awards to Noushin N

Popular Question 8 months ago, created a question with more than 1,000 views. For NGS preprocessing pipleine for ion torrent data
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Calculating Variant Allele Frequency
Great Question 10 months ago, created a question with more than 5,000 views. For Samtools Index Segmentation Fault
Popular Question 11 months ago, created a question with more than 1,000 views. For NGS preprocessing pipleine for ion torrent data
Scholar 12 months ago, created an answer that has been accepted. For A: Extract allele frequencies from VCF
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Calculating Variant Allele Frequency
Scholar 12 months ago, created an answer that has been accepted. For A: Extract allele frequencies from VCF
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Calculating Variant Allele Frequency
Popular Question 15 months ago, created a question with more than 1,000 views. For NGS preprocessing pipleine for ion torrent data
Appreciated 18 months ago, created a post with more than 5 votes. For Somatic mutation calling without matched normal
Scholar 2.2 years ago, created an answer that has been accepted. For A: Extract allele frequencies from VCF
Scholar 2.4 years ago, created an answer that has been accepted. For A: Extract allele frequencies from VCF
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Mutect Allele Counts Vs Mpileup
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Mutect Allele Counts Vs Mpileup
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Somatic mutation calling without matched normal
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Somatic Mutation Phasing
Student 3.7 years ago, asked a question with at least 3 up-votes. For Somatic mutation calling without matched normal
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Parsing Base String From Samtools Mpileup
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Parsing Base String From Samtools Mpileup
Supporter 4.9 years ago, voted at least 25 times.

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