User: Floris Brenk

gravatar for Floris Brenk
Floris Brenk750
Reputation:
750
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Trusted
Location:
USA
Last seen:
1 day, 6 hours ago
Joined:
3 years, 2 months ago
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Posts by Floris Brenk

<prev • 148 results • page 1 of 15 • next >
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Comment: C: How to annotate TTS or TES
... If you got human or mouse data, you could download the FANTOM5 (http://fantom.gsc.riken.jp/data/) annotated promoters and use an intersecting tool to annotate your start sites with that. ...
written 8 days ago by Floris Brenk750
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tool for identifying structural variation for DNA
... Hi all, I have a large stretch of DNA (about 75 kb) and I suspect there is some structural variation in there like duplications and maybe inversions. Also maybe this variation is already a bit "old" (meaning happened a long time ago thru evolution) so e.g. duplications are likely not to be 100% iden ...
cnv dna written 8 days ago by Floris Brenk750
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Answer: A: Which SNPs fall within genes and what's their description?
... http://bedtools.readthedocs.io/en/latest/content/tools/intersect.html > intersectBed -a file1 -b file2 -wb ...
written 9 days ago by Floris Brenk750
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Comment: C: RNA seq library preparation, PCR cycles
... I depends a bit on your experimental design meaning do you have 5 cases and 5 controls and all controls have more PCR cycles then yes it might be an issue. So maybe elaborate a bit more about the project and planned analyses... ...
written 11 days ago by Floris Brenk750
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Comment: C: vcftools merge files problem
... Then try to remove this line and merge again... does this works? grep -v "19:41725108" yourvcffile > tempfile.vcf ...
written 9 weeks ago by Floris Brenk750
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Comment: C: vcftools merge files problem
... "Wrong number of values in SS6004477/PL at 19:41725108 .. nAlleles=1, nValues=3." "Wrong number of values in SS6004477/PL at 19:41725108" So you have too many values at bp 19:41725108 doing grep "19:41725108" yourvcffile > tempfile.txt then you check what is wrong ...
written 9 weeks ago by Floris Brenk750
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Comment: C: risk value with genetic data
... You mean "genetic risk score"? just google this and many software and explanations are available ...
written 10 weeks ago by Floris Brenk750
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Answer: A: continuos covariates in Plink
... Usually people use them 0 or 1 coded, but this also depends on the number of races you have? For age this depends on the phenotype you have.. For example when you have an age related phenotype like Alzheimer's then you just use age as a continuous covariate. Overall, it might also be good to add th ...
written 10 weeks ago by Floris Brenk750
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Answer: A: How to convert Illumina top/bot SNPs to forward/reverse?
... Check this out: http://gengen.openbioinformatics.org/en/latest/tutorial/coding/ ...
written 11 weeks ago by Floris Brenk750
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Comment: C: Ped file contains: 0, -, multibase SNPs, and reverse order genotypes
... --- In addition some SNPs contain multiple base pairs e.g GAT. -> These are insertions or deletions How much of the 0 genotypes and other genotypes remain if you filter for example on --geno and --maf etc ? They should be all gone then... plink --file INPUT --maf 0.05 --geno 0.05 --hwe 1e-6 -- ...
written 11 weeks ago by Floris Brenk750

Latest awards to Floris Brenk

Scholar 8 days ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Student 3 months ago, asked a question with at least 3 up-votes. For Reformat minimac imputated files to plink file
Voter 4 months ago, voted more than 100 times.
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Difference Between Gene Expression And Transcript Expression
Scholar 6 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Scholar 7 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Centurion 9 months ago, created 100 posts.
Scholar 9 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Popular Question 10 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Appreciated 11 months ago, created a post with more than 5 votes. For A: Difference Between Gene Expression And Transcript Expression
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Popular Question 14 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Popular Question 16 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Popular Question 16 months ago, created a question with more than 1,000 views. For Snp Coordinates Hg19, Hg18, Hg17 Changed But Also Closest Genes Etc
Popular Question 16 months ago, created a question with more than 1,000 views. For SNP in Transcription factor binding site analysis
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Popular Question 18 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Scholar 2.1 years ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: 1000 Genomes Ld Calculation
Scholar 2.8 years ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
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Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Difference Between Gene Expression And Transcript Expression

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