User: Marvin

gravatar for Marvin
Marvin150
Reputation:
150
Status:
Trusted
Location:
Australia
Last seen:
1 day, 21 hours ago
Joined:
4 years, 5 months ago
Email:
d****@gmx.de

Posts by Marvin

<prev • 52 results • page 1 of 6 • next >
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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 2 days 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 2 days 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 days ago by Marvin150 • updated 2 days ago by Kevin Blighe52k
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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 8 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 8 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 8 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 8 months ago by Marvin150
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Comment: C: Difference between various GRCH 37 releases?
... I don't understand this ... let's say in p6 there are 3 repeats on chromosome 17. Then in p7 there are 4 repeats. In the fasta file the sequence "> chr17" will thus be 1 repeat longer and thus all the nucleotides after that additional repeat will have a changed coordinate? You say that the three ...
written 12 months ago by Marvin150
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Comment: C: Difference between various GRCH 37 releases?
... Hi Emily, a question regarding your last sentence: how can the primary assembly coordinates remain unaltered if you ADD something? let's say in the middle of chromosome 17 there is a sequence which contains 4 repeats and not 3, as previously thought. Thus I publish a patch and now there are 4 repeat ...
written 12 months ago by Marvin150
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Comment: C: snpEff: wrong HGVS output?
... yes, everything as expected here, c.-1032 is the correct HGVS notation (see the comments below Kevins answer) ...
written 14 months ago by Marvin150

Latest awards to Marvin

Popular Question 3 days ago, created a question with more than 1,000 views. For I don't understand bcftools call behaviour
Popular Question 8 months ago, created a question with more than 1,000 views. For I don't understand bcftools call behaviour
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Popular Question 14 months ago, created a question with more than 1,000 views. For I don't understand bcftools call behaviour
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: NGS mapper that supports IUPAC reference
Popular Question 2.4 years ago, created a question with more than 1,000 views. For I don't understand bcftools call behaviour
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Samtools mpileup: read base column symbols
Popular Question 2.4 years ago, created a question with more than 1,000 views. For IGV genome browser problems
Popular Question 2.4 years ago, created a question with more than 1,000 views. For NGS mapper that supports IUPAC reference
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Split BAM into 1 BAM per contig
Popular Question 4.0 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 4.0 years ago, created a question with more than 1,000 views. For IGV genome browser problems
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Get the consensus sequence ... (I know, should be easy)
Student 4.0 years ago, asked a question with at least 3 up-votes. For NGS mapper that supports IUPAC reference

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