User: nsmi8446

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nsmi8446120
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Posts by nsmi8446

<prev • 13 results • page 1 of 2 • next >
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Comment: C: How to Simulate RNA-Seq data with allelic bias
... If you're familiar with R this could be of value: http://www.bioconductor.org/packages/release/bioc/html/polyester.html ...
written 9 months ago by nsmi8446120
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Answer: A: Variant allele frequency
... Once you have your variant file you can filter variants based on allele frequency: https://vcftools.github.io/man_latest.html#BASIC%20OPTIONS See the section on allele filtering. Hope this helps. ...
written 10 months ago by nsmi8446120
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Answer: A: Can I align two DNA sequences using BLAST from command line?
... I think you want to create one database from one of the genomic sequences you have and blast the other different genomic sequence against it? If this is the case, you would create one database like you already have (let's say your two sequence files are called genomic.sequences.1.fasta and genomic ...
written 10 months ago by nsmi8446120 • updated 10 months ago by h.mon29k
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Comment: C: Allele specific expression analysis using human cell line
... All heterozygous sites will be bi-allelic. ...
written 10 months ago by nsmi8446120
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Comment: C: Allele specific expression analysis using human cell line
... You would know it's not monoallelic in the example above because the sample is heterozygous at this site. One allele would come from the mother (A) and the other allele (G) would come from the father. This site would be bi-allelic. ...
written 10 months ago by nsmi8446120
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Comment: C: Allele specific expression analysis using human cell line
... Then I don't think you can do it. In this scenario you have the following genotypes of the mother: ? / ? and father: ? / ? You will have the genotype of your sample (let's say A / G) but you will not be able to figure out which allele came from which parent and if allele specific expression is pre ...
written 10 months ago by nsmi8446120
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Comment: C: Allele specific expression analysis using human cell line
... Yes, let's say the mother has the following genotype: T / T and the father has the same genotype: T / T. Their offspring will all have the genotype T / T. How would you be able to tell whether the T came from only the mother or only the father? ...
written 10 months ago by nsmi8446120
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Answer: A: Allele specific expression analysis using human cell line
... You will need the parental genomes unfortunately. Without the parental genomes you will not be able to determine which allele comes from the mother and which allele comes from the father. ...
written 10 months ago by nsmi8446120
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Answer: A: miRNA differential expression
... This site might be helpful for you, it gives an accessible introduction to this type of analysis: https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/srna/tutorial.html ...
written 10 months ago by nsmi8446120
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Comment: C: Software for Tree Visualization
... I still come back to this response. Thank you! ...
written 10 months ago by nsmi8446120

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