User: misterie

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misterie90
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Posts by misterie

<prev • 77 results • page 1 of 8 • next >
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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 1 day 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 4 days ago by misterie90 • updated 4 days ago by Pierre Lindenbaum125k
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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$SNR, mixtureParams = cnSet@mixtureParams, : Recalibration not possible. Possible cause: small sample size. ...
written 4 months ago by misterie90
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Comment: C: crlmm package in R - processing the SNP6 copy number data error No arrays above
... Hi, thank you. There are 11 samples. ...
written 4 months ago by misterie90
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crlmm package in R - processing the SNP6 copy number data error No arrays above quality threshold!
... Hi, I am trying to analysis SNP6.0 copy number data. For this purpose I am using the crlmm package in R. The first steps look like; cnSet <- constructAffyCNSet(sinfo$celFiles, batch=rep(1, nrow(sinfo)),cdfName="genomewidesnp6", genome="hg19") cnrmaAffy ...
R snp6 copy number written 4 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 8 months ago by misterie90
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Comment: C: Testing uniform distribution of SNPs across chromosome
... Ok. Thank you. I still do not understand, why I can't use a uniform distribution to check whether the number of variants in windows (non-overlapping) is randomly distributed or is constant ...
written 8 months ago by misterie90
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Checking regions with high density of SNPs
... Hi, I calculated number of SNPs in non-overlapping windows in each chromosome. I found regions with extreme numbers of SNPs in compare to other windows. How can I check this region/window? What software can I use to check if this region contain many genes or sth else? I would like do it based on GF ...
snps high density written 8 months ago by misterie90
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Comment: C: Testing uniform distribution of SNPs across chromosome
... Thank you. Could you tell me where can I find information that to test inter-SNP distance I should use gamma distribution and Poisson distribution for number of snps in windows? I need a reference why I am using this distribution instead of uniform distribution. ...
written 8 months ago by misterie90
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Comment: C: Testing uniform distribution of SNPs across chromosome
... Thank You! I have another question. I have also information about distance of the snp to the cloest indel. Should I also use a gamma distribution to check whether snps are close to indels or if it is a randomness? And the same question about length of indels. To check whether long of indels (Bp) i ...
written 8 months ago by misterie90

Latest awards to misterie

Popular Question 8 months ago, created a question with more than 1,000 views. For Number of SNPs in VCF
Popular Question 8 months ago, created a question with more than 1,000 views. For Number of SNPs in VCF
Student 13 months ago, asked a question with at least 3 up-votes. For Convert two-column txt to multiple column csv
Popular Question 18 months ago, created a question with more than 1,000 views. For Cluster analysis for SNPs data in R
Popular Question 18 months ago, created a question with more than 1,000 views. For Comparing two columns and replace in R Package

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