User: charizanisk

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charizanisk10
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2 years, 11 months ago
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3 years, 9 months ago
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Posts by charizanisk

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Samtofastq: Net.Sf.Picard.Picardexception: "Found N Unpaired Mates "
... Hi guys,   I am getting a similar error. Here is what I'm trying to do. I have a lot of data but I want to focus on specific areas because the software I am using is crashing. So I go and use samtools to isolate certain coordinates: samtools view whatever_sorted.bam chr1:115240000-115270000 ch ...
written 3.6 years ago by charizanisk10
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Comment: C: Determining the sex of the fetus from plasma of the pregnant mother
... Thank you Karl, All the papers that I have seen out there use both maternal and paternal fgenotypes and use only parental-specific homozygous loci to determine the fetal DNA fraction and do the rest of the analysis. My problem is that we don't have the paternal genotype... aka we are fishing in the ...
written 3.8 years ago by charizanisk10
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Comment: C: CytoSNP12 minor allele frequency detection levels. How low can we go?
... Hi Jan, Thank you for helping me out here and I apologize for not being clear.   I did not design the experiment but a lab that designed it asked me to analyse the data. They have 12 patients (cancer patients) and they used this chip as a genotyping tool. Their goal is to find, for each patient, ...
written 3.8 years ago by charizanisk10
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CytoSNP12 minor allele frequency detection levels. How low can we go?
... Ok I a fairly new to both SNV calling and chip arrays. Most of my experience is with RNA-seq, alternative splicing etc. Now, I have some data from Illumina's Human CytoSNP12 bead array that I want to analyze. I used GenomeStudio and I got all the tables, and most of what I see makes sense. My only ...
array illumina cytosnp snp genomestudio written 3.8 years ago by charizanisk10
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Determining the sex of the fetus from plasma of the pregnant mother
... So many people have mentioned previously about seeing reads aligned in the Y chromosome when the sequencing data is from a female subject. So there are ways around it, such as masking PAR regions or excluding the Y chromosome from the study completely. I have the following challenge. What can you d ...
genome next-gen alignment snp written 3.8 years ago by charizanisk10

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