User: Christof Winter
Christof Winter • 990
- Reputation:
- 990
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- Trusted
- Location:
- Lund, Sweden
- Website:
- http://www.biotec.tu-d...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 5 years, 1 month ago
- Joined:
- 8 years, 7 months ago
- Email:
- c**************@med.lu.se
Posts by Christof Winter
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... 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 5.5 years ago by
Christof Winter • 990
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... I think unless there are contaminating cells in the culture, your cell line DNA extracts should be close to 100% pure.
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written 5.5 years ago by
Christof Winter • 990
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... See also https://www.biostars.org/p/65080/
...
written 5.5 years ago by
Christof Winter • 990
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... 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.
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written 5.5 years ago by
Christof Winter • 990
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... 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 5.5 years ago by
Christof Winter • 990
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... How do you handle multiple transcripts that produce different isoforms when assigning an amino acid position to a genomic position?
...
written 5.7 years ago by
Christof Winter • 990
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... ANNOVAR is your friend. If it's human, you could also try the web server at http://wannovar.usc.edu/.
...
written 5.7 years ago by
Christof Winter • 990
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... 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).
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written 6.5 years ago by
Christof Winter • 990
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... 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 6.5 years ago by
Christof Winter • 990
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... 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 6.5 years ago by
Christof Winter • 990
Latest awards to Christof Winter
Appreciated
5.7 years ago,
created a post with more than 5 votes.
For C: How To Determine If Paired–End Illumina Rnaseq Reads Are Strand–Specific
Appreciated
5.7 years ago,
created a post with more than 5 votes.
For A: Discrimination Between Germline And Somatic Mutations In Tumor Without The Avail
Good Answer
5.7 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
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5.7 years ago,
voted more than 100 times.
Supporter
5.7 years ago,
voted at least 25 times.
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5.7 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
5.7 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
5.7 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
5.7 years ago,
created an answer with at least 3 up-votes.
For A: Samtools Mpileup Vs Pileup: Multiple Samples And Gt=0/0
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5.7 years ago,
created an answer with at least 3 up-votes.
For A: Extract Expression Data For Candidate Gene List In Microarray
Teacher
5.7 years ago,
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For A: How To Find The Enriched Repeat Elements Between Two Sequences
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