User: Christof Winter

gravatar for Christof Winter
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Lund, Sweden
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Posts by Christof Winter

<prev • 51 results • page 1 of 6 • next >
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Comment: C: Somatic mutation calling without matched normal
... Yes, I would also say it's close to impossible to distinguish between novel somatic and private or rare germline variants that are not dbSNP/1000genomes/ESP6500. Looking at both mutation allele frequency and copy number at that position might help for cases where a somatic mutation occurred after a ...
written 4.9 years ago by Christof Winter980
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Comment: C: Somatic mutation calling without matched normal
... I think unless there are contaminating cells in the culture, your cell line DNA extracts should be close to 100% pure. ...
written 4.9 years ago by Christof Winter980
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Comment: C: Somatic mutation calling without matched normal
... See also https://www.biostars.org/p/65080/ ...
written 4.9 years ago by Christof Winter980
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Comment: C: Somatic mutation calling without matched normal
... Note that the variant allele frequencies will be shifted from 50%/100% even in a pure tumor such as a cell line if you have copy number alterations. Depending on the cancer type, cancer cell lines can easily be triploid or tetraploid, with many copy number aberrations. ...
written 4.9 years ago by Christof Winter980
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Answer: A: Somatic mutation calling without matched normal
... Since you are asking about cell lines, maybe these have already been sequenced. There are bigger studies I'm aware of: Cancer Cell Line Encyclopedia (CCLE), see http://www.ncbi.nlm.nih.gov/pubmed/22460905 Browse and download the data: http://www.broadinstitute.org/ccle/home NCI-60 cell line, se ...
written 4.9 years ago by Christof Winter980
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Comment: C: How To Obtain Protein Or Uniprot Coordinates From Chromosomal Coordinates?
... How do you handle multiple transcripts that produce different isoforms when assigning an amino acid position to a genomic position? ...
written 5.1 years ago by Christof Winter980
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Answer: A: How To Obtain Protein Or Uniprot Coordinates From Chromosomal Coordinates?
... ANNOVAR is your friend. If it's human, you could also try the web server at http://wannovar.usc.edu/. ...
written 5.2 years ago by Christof Winter980
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Comment: C: How Likely Are Two Sequences To Have The Same Snps By Chance?
... Note also that the human reference genome itself contains rare SNPs. As a result, at these loci the probability that any two unrelated individuals will have the same non-reference base is very high (since the reference base is the rare allele, and the individuals simply have the common allele). ...
written 5.9 years ago by Christof Winter980
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Comment: C: How Likely Are Two Sequences To Have The Same Snps By Chance?
... It only becomes a variant of the birthday paradox if you are asking if in a pool of sequences, there are two that share a SNP. ...
written 5.9 years ago by Christof Winter980
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Answer: A: Adaptor Order In Pe Sequencing On Illumina Hiseq
... Swapping the adapter orders will merely swap read1 and read2 of your sequencing results. primers going outwards instead of ampiying into the region I want No, the primer has in inherent order -- polymerase always adds at the 3' end of the primer. So if your primer design is right, there is no way ...
written 5.9 years ago by Christof Winter980

Latest awards to Christof Winter

Good Answer 5.1 years ago, created an answer that was upvoted at least 5 times. For A: Discrimination Between Germline And Somatic Mutations In Tumor Without The Avail
Voter 5.1 years ago, voted more than 100 times.
Supporter 5.1 years ago, voted at least 25 times.
Commentator 5.1 years ago, created a comment with at least 3 up-votes. For C: How To Determine If Paired–End Illumina Rnaseq Reads Are Strand–Specific
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Get A Graphical Representation Of Number Of Reads In Bam File For A Certain Geno
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Discrimination Between Germline And Somatic Mutations In Tumor Without The Avail
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Samtools Mpileup Vs Pileup: Multiple Samples And Gt=0/0
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Extract Expression Data For Candidate Gene List In Microarray
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: How To Find The Enriched Repeat Elements Between Two Sequences

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