User: misterie

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misterie90
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Posts by misterie

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Comment: C: Amplicon sequencing and unwanted amplicons
... I mean that variants called on one chromosome are localized in two totally apart genes. Only amplicon from one of these two genes was sequenced. ...
written 7 months ago by misterie90
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Comment: C: Amplicon sequencing and unwanted amplicons
... Yes, I did. Primers are uniquely amplifying region. I see, that the mapping quality in these regions is very high. Do you have any other ideas? ...
written 7 months ago by misterie90
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Amplicon sequencing and unwanted amplicons
... Hi, I have sequenced amplicons of genes on different chromosomes in order to call variants. I noticed, that many sequences were mapped to another region in the genome –– on a chromosome that should contain only one amplicon, but I get variants for two genes that overlapped different regions of this ...
amplicon sequencing unwanted written 7 months ago by misterie90
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snpEff and SIFT calculation
... Hi, I annotated my VCF files using snpEff by creating new database (I use own assembly and gtf file). I would like also to calculate SIFT (prediction of consequence in missense variant). I found, that I can do this using snpSift, but I see that I need to use dbNSFP that is dedicated for human geno ...
sift snpeff written 7 months ago by misterie90
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Translate amino acid mutation to the nucleotide with position in reference genome
... Hi I would like to use samtools view to extract reads that overlap position of given mutation. Unfortunately I have information about mutations of ESR1 in the amino acid code, like: Y541S and D542G. How can I use this information to extract SNV mutations from my BAM files? Thanks. ...
mutation written 10 months ago by misterie90
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Number of transcript reads with given mutation
... Hi, I have a list with a specific mutations localised on one gene. I have 100 BAM RNA-seq samples, mapped to the reference genome. Let's assume, that I want to calculate number of transcript reads with a specific mutation (SNV), e.g. A/T that is localised at 120 position of gene (e.g. BRCA1). How c ...
rna-seq snp written 10 months ago by misterie90 • updated 10 months ago by Pierre Lindenbaum131k
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Comment: C: crlmm package in R - processing the SNP6 copy number data error No arrays above
... Thank you. I checked these parameters. Now I increased the number of samples to 80 and I get just a warning: Warning message: In crlmmGT2(A = A(cnSet), B = B(cnSet), SNR = cnSet$SNR, mixtureParams = cnSet@mixtureParams, : Recalibration not possible. Possible cause: small sample size. ...
written 15 months ago by misterie90
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Comment: C: crlmm package in R - processing the SNP6 copy number data error No arrays above
... Hi, thank you. There are 11 samples. ...
written 15 months ago by misterie90
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crlmm package in R - processing the SNP6 copy number data error No arrays above quality threshold!
... Hi, I am trying to analysis SNP6.0 copy number data. For this purpose I am using the crlmm package in R. The first steps look like; cnSet <- constructAffyCNSet(sinfo$celFiles, batch=rep(1, nrow(sinfo)),cdfName="genomewidesnp6", genome="hg19") cnrmaAffy ...
R snp6 copy number written 15 months ago by misterie90
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Comment: C: Testing uniform distribution of SNPs across chromosome
... Ok, thank you! Now I understand, but which value should I use for lambda in Poisson distribution. I would like to test this using Kolmogorov-Smirnov. I have vector with number of SNPs in each 100kb non-overlapping windows, but for testing whether the numer of SNPs is random (random number of SNPs = ...
written 18 months ago by misterie90

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