User: Marvin

gravatar for Marvin
Marvin150
Reputation:
150
Status:
Trusted
Location:
Australia
Last seen:
1 month, 4 weeks ago
Joined:
4 years, 9 months ago
Email:
d****@gmx.de

Posts by Marvin

<prev • 55 results • page 1 of 6 • next >
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Comment: C: Complementary strand in cluster generation
... I have the same question and I don't think the question was really answered. You have a double-stranded fragment, Adapter1 on one side and Adapter2 on the other side. Now you dehybridize. Let's say on the flow cell there is ONLY the complement to Adapter1. But BOTH single-stranded fragments have Ada ...
written 9 weeks ago by Marvin150
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Comment: C: Does allele refer to the entire gene sequence or one position of the gene sequen
... Thank you Emily, I love it when things are put into historical context. That makes the process of (truly) understanding a complete one. ...
written 10 weeks ago by Marvin150
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Comment: C: Is 1 deleted T in a T stretch always detected, assuming enough coverage of cours
... I totally forgot about the step "indel realignment" in GATK best practices. I think that is exactly the step which avoids the problem I've described above. Even in a scenario where the programmer had opted for choosing a random T for each read, the probability for that worst-case distribution which ...
written 3 months ago by Marvin150
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Comment: C: Is 1 deleted T in a T stretch always detected, assuming enough coverage of cours
... "I guess you simply do not have a variant and all you see are artifacts" -> No, in my made up example the biological truth is that there is 1 T deleted. And all reads are perfetly fine without artifacts. The question is, what does the mapper do with regards to asking the question "which T do I ma ...
written 3 months ago by Marvin150
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Comment: C: Is 1 deleted T in a T stretch always detected, assuming enough coverage of cours
... Thank you but that is not the problem that I have described. I know the text is a little bit long but I'm talking about unfortunate mapping which might lead to not even seeing a variant. The link instead describes what to do after seeing the same variant in different callers. ...
written 3 months ago by Marvin150
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Is 1 deleted T in a T stretch always detected, assuming enough coverage of course?
... Let's assume the following reference sequence: ATTTTTTTTTTTTTTTTTTTTA The individual has a deletion of 1 T in that stretch of 20 T's. Could be the left-most, the middle, the right-most. We don't know. Let's assume I have sequenced 100 reads which cover that region. So the mapper has to make a cho ...
stretch caller mapper written 3 months ago by Marvin150 • updated 3 months ago by Kevin Blighe56k
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Comment: C: Download hg19 from NCBI FTP
... Oh thank you, now I know why I couldn't find it. I wouldn't have guessed that it is wrong to navigate to "genomes" from the top level. **EDIT** I just realized that the other thread was mine, lol. I've accepted your answer on the other thread. ...
written 12 months ago by Marvin150
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Comment: C: Download hg19 from NCBI FTP
... No, you posted a link instead of explaining how/where to navigate inside the FTP browser. I want to educate myself and not ask someone for a link everytime. "Where are you looking" -> I'm looking at the link that I've posted. ...
written 12 months ago by Marvin150
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Comment: C: Download hg19 from NCBI FTP
... Thank you but that thread doesn't answer the question? They refer to Ensembl instead. I want to know where I can find the right file on the NCBI FTP? ...
written 12 months ago by Marvin150
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(Closed) Download hg19 from NCBI FTP
... I have scanned through ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/ but I cannot find the reference sequence hg19? ...
ncbi ftp hg19 written 12 months ago by Marvin150

Latest awards to Marvin

Supporter 9 weeks ago, voted at least 25 times.
Popular Question 3 months ago, created a question with more than 1,000 views. For I don't understand bcftools call behaviour
Popular Question 12 months ago, created a question with more than 1,000 views. For I don't understand bcftools call behaviour
Popular Question 12 months ago, created a question with more than 1,000 views. For Samtools mpileup: read base column symbols
Popular Question 12 months ago, created a question with more than 1,000 views. For IGV genome browser problems
Popular Question 18 months ago, created a question with more than 1,000 views. For I don't understand bcftools call behaviour
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: NGS mapper that supports IUPAC reference
Popular Question 2.7 years ago, created a question with more than 1,000 views. For I don't understand bcftools call behaviour
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Samtools mpileup: read base column symbols
Popular Question 2.7 years ago, created a question with more than 1,000 views. For IGV genome browser problems
Popular Question 2.7 years ago, created a question with more than 1,000 views. For NGS mapper that supports IUPAC reference
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Split BAM into 1 BAM per contig
Popular Question 4.3 years ago, created a question with more than 1,000 views. For FASTA of an arbitrary genome: Is the first base the 5' end?
Popular Question 4.3 years ago, created a question with more than 1,000 views. For IGV genome browser problems
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Get the consensus sequence ... (I know, should be easy)
Student 4.3 years ago, asked a question with at least 3 up-votes. For NGS mapper that supports IUPAC reference

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