User: schmoo

gravatar for schmoo
schmoo30
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30
Status:
New User
Location:
Germany
Last seen:
1 year, 10 months ago
Joined:
4 years, 1 month ago
Email:
m*****************@medma.uni-heidelberg.de
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Posts by schmoo

<prev • 5 results • page 1 of 1 • next >
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Comment: C: Variant Effect Prediction for Custom Genomes (A.Fumigatus)
... Thanks for the hint! I already checked VEP from Ensembl but it seems to lack any information about PolyPhen/SIFT etc. (or I couldn't find it?). However, I found SIFT databases for A.fumigatus on (surprise) the SIFT homepage which can be easily adapted for annotation using ANNOVAR: http://sift-db.bi ...
written 3.0 years ago by schmoo30
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Comment: A: Variant Effect Prediction for Custom Genomes (A.Fumigatus)
... Thanks for the feedback Charles! I already worked with SnpEff and it does annotate variants nicely. But my problem is rather to create a protein effect database that can be used by SnpEff/ANNOVAR to annotate a given (amino acid changing) variant with the predicted effect on the protein, e.g. damagi ...
written 3.0 years ago by schmoo30
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Variant Effect Prediction for Custom Genomes (A.Fumigatus)
... Dear all, currently, I am analyzing variants in genomes of Aspergillus Fumigatus strains and would like to predict the consequences of amino acid changes/frameshifts etc. For human genome data I am familiar with SIFT/PolyPhen etc. and routinely use that for annotation using ANNOVAR. So far, I coul ...
genome sequencing written 3.0 years ago by schmoo30
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sciClone package -> mosaic copy number correction of VAFs?
... Dear all, I'm using the sciClone R package and got very exciting data with that! Now I am wondering if anyone has experience in attributing non-integer values to the copynumber segments in which the measured VAFs are located. Given that I am confident to measure an accurate copynumber value of 1.5 ...
tumor heterogeneity sciclone copy number variation written 4.1 years ago by schmoo30 • updated 4.1 years ago by Chris Miller20k
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Comment: C: cn.mops - Error in if (n > 512) n <- 2^ceiling(log2(n))
... Hi emmasreid, I was struggling with the very same problem for a few days now and I think I came over it a few hours ago... simply switch to mode="paired" in getSegmentReadCountsFromBAM and you will eventually get read count values in "X" for your samples. A look into the Table S3 of this paper (htt ...
written 4.2 years ago by schmoo30

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Popular Question 3.0 years ago, created a question with more than 1,000 views. For sciClone package -> mosaic copy number correction of VAFs?
Autobiographer 4.2 years ago, has more than 80 characters in the information field of the user's profile.

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