User: Manuel Landesfeind

Reputation:
1,120
Status:
Trusted
Location:
Freiburg, Germany
Last seen:
12 hours ago
Joined:
2 years, 9 months ago
Email:
l**********@gmail.com

Posts by Manuel Landesfeind

<prev • 115 results • page 1 of 12 • next >
0
votes
0
answers
88
views
0
answers
Comment: C: Appropriate methodologies of comparing whole exome sequencing data between circu
... I agree, in that case you should not use tumor as normal. But than I would still go forward with calling mutations on all samples and removing everything found in population databases with decent frequency. ...
written 7 days ago by Manuel Landesfeind1.1k
1
vote
0
answers
88
views
0
answers
Comment: C: Appropriate methodologies of comparing whole exome sequencing data between circu
... About the somatic variants: you can annotate with ExAC (or other population databases) to remove "putative germline" from your analysis. There are plenty of suggestions on Biostars already. Second, depending on your scientific question, it might be sufficient to use the "tumor" as "normal" because y ...
written 7 days ago by Manuel Landesfeind1.1k
0
votes
1
answer
13k
views
1
answers
Comment: C: what is the difference between GRCh37 and hg19 ?
... The term "GRCh38" refers to the genomic assembly. The ".78" and ".91" refer to the version of gene annotation provided by Ensembl, i.e. where do introns/exons/etc start and end. To my knowledge, the genomic sequence for "GRCh38.78" and "GRCh38.91" should be identical and only the gene annotation sho ...
written 9 days ago by Manuel Landesfeind1.1k
0
votes
3
answers
371
views
3
answers
Answer: A: Another statistical model to estimate gene/transcript expression
... @Asaf already mentioned that the topic is well-studied and I agree that little improvements will have little impact. In particular if you have to demonstrate economic impact in your proposal. Industry likes de facto standards and well-established and often-used methods. I work in a CRO with all ki ...
written 7 months ago by Manuel Landesfeind1.1k
0
votes
1
answer
778
views
1
answers
Comment: C: Somatic Mutation Identification for Tumor without Normal
... Thats interesting... for some reason I thought it would be hg38... don't know why.. ...
written 11 months ago by Manuel Landesfeind1.1k
2
votes
1
answer
778
views
1
answers
Comment: C: Somatic Mutation Identification for Tumor without Normal
... What can be discussed is the threshold you use: when do you consider a variant as putative germline? 1%, 10%, ... allelic frequency? In any population or overall? PS: If you figure out a good threshold or some literature, please share here because it will save me some time to evaluate this by mysel ...
written 11 months ago by Manuel Landesfeind1.1k
1
vote
1
answer
778
views
1
answers
Comment: C: Somatic Mutation Identification for Tumor without Normal
... I absolutely agree with Titus that gnomAD and ExAC are key databases. We use 1000G, HapMap and others because our established pipeline uses hg19 genome assembly. Moving to hg38 and corresponding databases is in progress and I plan to use gnomAD and ExAC too. ...
written 11 months ago by Manuel Landesfeind1.1k
0
votes
1
answer
778
views
1
answers
Answer: A: Somatic Mutation Identification for Tumor without Normal
... For me the number of mutations in your tumors seems suspiciously high. We do a very similar approach in removing potential germline mutations from tumors lacking matched normal samples (using different annotation databases and no internal normal-pool). In our models we usually retain between 500 an ...
written 11 months ago by Manuel Landesfeind1.1k
0
votes
2
answers
452
views
2
answers
Comment: C: Variant calling from multiple sequencing runs for a single samples
... What do you want to demonstrate with the study? If you are interested in the biological results (i.e., what are the mutations of your biological sample) I recommend combining on the BAM level. This will increase the total coverage and thus gives you a higher accuracy for variant detection. In partic ...
written 12 months ago by Manuel Landesfeind1.1k
0
votes
2
answers
452
views
2
answers
Comment: C: Variant calling from multiple sequencing runs for a single samples
... > ... I wasn't using a large bam file containing all of these libraries was that it was taking too much time to crunch What does that mean? Can you lay out the details of the sequencing a little bit more? How do these different libraries compare? Do you consider them technical replicates? Or wa ...
written 12 months ago by Manuel Landesfeind1.1k

Latest awards to Manuel Landesfeind

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Appreciated 7 months ago, created a post with more than 5 votes. For C: Stop to make GUI with Java .... Use Qt 5 !!
Appreciated 10 months ago, created a post with more than 5 votes. For C: Stop to make GUI with Java .... Use Qt 5 !!
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Guru 12 months ago, received more than 100 upvotes.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Centurion 13 months ago, created 100 posts.
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Scholar 18 months ago, created an answer that has been accepted. For A: Changing the header of a VCF file and the field correspondingly
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: Splice aware aligner - what does it mean?
Scholar 22 months ago, created an answer that has been accepted. For A: Changing the header of a VCF file and the field correspondingly
Scholar 22 months ago, created an answer that has been accepted. For A: Changing the header of a VCF file and the field correspondingly
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Appreciated 2.2 years ago, created a post with more than 5 votes. For C: Stop to make GUI with Java .... Use Qt 5 !!
Scholar 2.2 years ago, created an answer that has been accepted. For A: Changing the header of a VCF file and the field correspondingly
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Voter 2.2 years ago, voted more than 100 times.
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: How to deal with many uncharacterized protein in the blastx results?
Scholar 2.3 years ago, created an answer that has been accepted. For A: Changing the header of a VCF file and the field correspondingly
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: How to cache reads?
Commentator 2.4 years ago, created a comment with at least 3 up-votes. For C: How to deal with many uncharacterized protein in the blastx results?
Appreciated 2.4 years ago, created a post with more than 5 votes. For C: Stop to make GUI with Java .... Use Qt 5 !!
Commentator 2.4 years ago, created a comment with at least 3 up-votes. For C: How to deal with many uncharacterized protein in the blastx results?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1097 users visited in the last hour