User: Matthias

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Matthias20
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Location:
Germany
Website:
http://matthiasmunz.de/
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3 days, 20 hours ago
Joined:
6 years, 11 months ago
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m************@gmx.de

Posts by Matthias

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Duplication rate differs up to 30% from that of Fastqc for single end reads
... Did you even read my question? ;-) It's not about the duplication rate in general, but the huge difference between Fastqc and Fastp. ...
written 3 days ago by Matthias20
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Duplication rate differs up to 30% from that of Fastqc for single end reads
... I found a quite big difference in the duplication between Fastp and Fastqc. For all my ~40 SE RNAseq samples, the rate is around 10-30% lower in Fastp compared to Fastqc. Is there an explanation for this and which one should trust more for RNAseq data? In this scatterplot, the duplication rates for ...
fastp rna-seq fastqc written 4 days ago by Matthias20
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Comment: C: Keep Format and Individual fields when annotating VCF with VEP
... Is there a way to convert the VEP annotated vcf to tab? ...
written 18 months ago by Matthias20
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Variant training set for Zebrafish to apply GATK VariantRecalibrator
... I am working genotyping-by-sequencing data of Zebrafish and it seems that there is no training/truth variant set available for applying GATK Variant Quality Score Recalibration (VQSR). I only found the dbSNP vcf files. Has anyone performed VQSR on Zebrafish data and/or can suggest a good variant s ...
gatk ngs zebrafish genotyping-by-sequencing snp written 2.2 years ago by Matthias20
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Answer: A: How to get the beginning and end-positions of a QTL-interval after doing QTL-ana
... Supposing you run scan1 (name of return object is `data.scan1`) on your data and want to get the 95% confidence interval (upper and lower marker) for the peak on chromosome `1`, type CI = bayesint(data.scan1, chr=1, prob=0.95) lower_marker = find.marker(data, chr=CI[1,1], pos=CI[1,2]) ...
written 3.0 years ago by Matthias20
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Is allele switching necessary before QTL mapping can be performed?
... I would to like do QTL mapping using genotypes of a F2 mouse generation which was derived by intercrossing from F0. F0 consists of individuals from two homozygous strains x and y. In my genotype file each marker has AA, AB or BB as possible genotype. However, allele A is not necessarily from strain ...
qtl mapping written 3.2 years ago by Matthias20
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Comment: C: QTL mapping vs. Association mapping for bi-parental crosses
... Hi Vincent, I know this post already. However, my questions are not answered by it. Maybe you can add some information here? ...
written 3.4 years ago by Matthias20
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QTL mapping vs. Association mapping for bi-parental crosses
... I have got genotype data of ~200 F2 samples which where derived from two grandparents (F0) AA and BB, and intercrossed (AB x AB) parents in the F1 generation. In order to detect loci that are associated with a continuous phenotype, typically, one performs a QTL mapping. Does an additional associa ...
qtl mapping written 3.4 years ago by Matthias20
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Answer: A: Downloading synonyms for dbSNP rsids
... You can download a list of "main" rsIds and their synonyms according to the latest Ensembl version here: http://genehopper.ifis.cs.tu-bs.de/downloads Hope, this helps. ...
written 4.9 years ago by Matthias20 • updated 10 months ago by RamRS30k
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Comment: C: Flip Gwas Data To Positive Strand (Hg19 Build 37)
... So your tool labels all SNPs with AT or GC as ambigous (meaning to delete them)? Deciding whether AT or GC has to be flipped or not is the major issue in the flipping process. Since you delete them all, you don't give a solution for that. ...
written 5.2 years ago by Matthias20

Latest awards to Matthias

Popular Question 18 months ago, created a question with more than 1,000 views. For Where To Find Pre-Computed Gene-To-Gene-Similarities Based On Gene Ontology (Go)
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Where To Find Pre-Computed Gene-To-Gene-Similarities Based On Gene Ontology (Go)
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Access Abstract From Pubmed Using Bio::Db::Eutilities

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