User: Michael Kosicki

Reputation:
80
Status:
New User
Location:
Wellcome Trust Sanger Institute
Last seen:
2 months ago
Joined:
3 months, 3 weeks ago
Email:
m***@sanger.ac.uk

Posts by Michael Kosicki

<prev • 11 results • page 1 of 2 • next >
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Answer: A: vcf files - extract SNPs
... If the first column is the "genes", then: bedtools intersect -wa -wb -a 1.vcf -b 2.vcf > shared.vcf grep -v '^#' shared.vcf | cut -f1 -d' ' shared.vcf | sort | uniq # list of unique genes Then, assuming it's the same reference (ie ref is the same on the same position) and that both vcf ...
written 3 months ago by Michael Kosicki80
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Comment: C: Changing the reference haplotype in VCF
... Sure, go ahead, thanks. ...
written 3 months ago by Michael Kosicki80
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Answer: C: Changing the reference haplotype in VCF
... Ok, I think I've found the solution myself: ## get mouse chr19 curl ftp://ftp.ensembl.org/pub/release-91/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.chromosome.19.fa.gz > chr19.fa.gz zcat chr19.fa.gz > chr19.fa ## get BALBc SNPs curl ftp://ftp-mouse.sanger.ac.uk/cu ...
written 3 months ago by Michael Kosicki80
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Comment: C: Changing the reference haplotype in VCF
... I think I might not have made myself clear. Consider a fasta reference "ref1" and a vcf file "vcf1" such that replacing all the variants in "ref1" with ones in "vcf1" gives me an alternative reference "ref2", which may have more or less nucleotides than "ref1" depending on the types of indels in "v ...
written 3 months ago by Michael Kosicki80
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Comment: C: Confidence Interval in R
... Look here: http://seqanswers.com/forums/showthread.php?p=161824 In short, every test functions under certain assumptions. Breaking those assumptions breaks the test. RNA-seq data breaks the assumption of the t-test that the data is drawn from a normal distribution. In practice, you'd fail to detect ...
written 3 months ago by Michael Kosicki80
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Comment: C: Confidence Interval in R
... Look up "edgeR" or "DESeq2" for differential gene expression testing on RNA-seq data. T-test is not appropriate in this situation, due to the way data is distributed (also, you probably need to normalize for sequencing depth between samples). P-value of a test is not a function of the confidence in ...
written 3 months ago by Michael Kosicki80
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Comment: C: Changing the reference haplotype in VCF
... I don't get it. Consider ATC>ATGCT with indels 2 T TG and 3 C CT. "Inverse" indels are 2 TG T and 4 CT C - second one shifted due to the first one "adding" sequence. ...
written 3 months ago by Michael Kosicki80
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Comment: C: Changing the reference haplotype in VCF
... I need to also "invert" the indels, this script seems to ignore them and only "invert" the SNPs. ...
written 3 months ago by Michael Kosicki80
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Comment: C: Changing the reference haplotype in VCF
... Could you elaborate? This tool just "merges" reference fasta and a vcf file, and does not produce a new vcf file, as far as I can tell. ...
written 3 months ago by Michael Kosicki80
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Answer: A: Sanger Sequencing showing too much background noise?
... If I understood correctly, they have performed a PCR on the material and then Sanger sequenced the product. 1) The sequencing service provider usually specifies, whether the product needs to be purified (e.g. using beads or columns) or whether they can do it for you (usually for a fee) and how much ...
written 3 months ago by Michael Kosicki80

Latest awards to Michael Kosicki

Scholar 11 weeks ago, created an answer that has been accepted. For C: Changing the reference haplotype in VCF
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: vcf files - extract SNPs
Scholar 3 months ago, created an answer that has been accepted. For C: Changing the reference haplotype in VCF

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