User: Floris Brenk

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Floris Brenk790
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790
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USA
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3 years, 10 months ago
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Posts by Floris Brenk

<prev • 172 results • page 1 of 18 • next >
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Comment: C: ATACseq and HiC sequencing
... Great thanks all for your help, much appreciated! Got one more additional questions, is there any need to PhiX spike-in during HiC or ATAC sequencing? or can the libraries just go on hiseq without issues? ...
written 11 days ago by Floris Brenk790
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Comment: C: ATACseq and HiC sequencing
... Was thinking about this method [HiC2][1] Very clear paper and protocol but no guidelines on sequencing depth... Just one sentence "Datasets from Rao et al. were selected solely based on their read depth that was comparable to datasets obtained with Hi-C 2.0 (100–200 million reads)" [1]: https://w ...
written 13 days ago by Floris Brenk790
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ATACseq and HiC sequencing
... Hi there, We are looking into ATACseq and HiC sequencing of some human derived samples. Does anyone has any recommendation about sequencing depth? e.g. how many samples to pool per lane on Illumina HiSeq. Have been looking around but no real data is present on this. Also is there some best practice ...
atac hic written 13 days ago by Floris Brenk790 • updated 13 days ago by Devon Ryan71k
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Comment: C: How to make a nice mutation overview figure like this?
... Also very nice thanks! ...
written 8 weeks ago by Floris Brenk790
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Answer: A: How to make a nice mutation overview figure like this?
... In the end I think this is the easiest way -> [Lollipops][1] [1]: https://github.com/pbnjay/lollipops ...
written 8 weeks ago by Floris Brenk790
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Comment: C: How to make a nice mutation overview figure like this?
... Looks very pretty and interesting thanks! I only have ~50 mutations per gene so I think the circos plot is a bit too complicated to show for those genes... ...
written 8 weeks ago by Floris Brenk790
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How to make a nice mutation overview figure like this?
... Hi all, Does anyone know how to make a nice mutation overview figure like this [nice figure][1]? I found a similar way to make these plots with [GenVisR][2] But was curious whether there are also other packages out there? Thanks Floris [1]: http://jamanetwork.com/data/Journals/NEUR/935945/nbs1 ...
R written 8 weeks ago by Floris Brenk790
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PCA matching controls with cases using genotypes
... Hi there, I have a relatively small dataset of cases (n=~800) and a very large amount of controls (n=~8000) in plink format. Now I would like to have the case-control ration 1:3 for further analysis. I was wondering is there a method or are there scripts available that perform some kind of PCA matc ...
pca plink written 9 weeks ago by Floris Brenk790
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Answer: A: Duplicate ID in bed file
... Using --list-duplicate-vars you can identify the duplicates in the data [plink website identifying duplicates][1] And using --exlcude you can remove your snps [plink website removing snps][2] [1]: https://www.cog-genomics.org/plink/1.9/data#list_duplicate_vars [2]: https://www.cog-genomics.or ...
written 10 weeks ago by Floris Brenk790
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Output the call rate of genotypes in plink
... Hi all, I was wondering whether someone knows an easy solution to output the call rate per individual from a plink file. I know you can filter on the call rate using --mind, but I would like to have a list with the call rate per sample. I tried some coding myself by taking each sample by itself and ...
plink written 12 weeks ago by Floris Brenk790 • updated 12 weeks ago by chrchang5232.7k

Latest awards to Floris Brenk

Popular Question 13 days ago, created a question with more than 1,000 views. For Coverage plots of gvcf files
Scholar 8 weeks 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 3 months ago, created a question with more than 1,000 views. For Coverage plots of gvcf files
Popular Question 8 months ago, created a question with more than 1,000 views. For Snp Coordinates Hg19, Hg18, Hg17 Changed But Also Closest Genes Etc
Scholar 8 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 11 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Student 11 months ago, asked a question with at least 3 up-votes. For Reformat minimac imputated files to plink file
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Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Difference Between Gene Expression And Transcript Expression
Scholar 14 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 14 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Scholar 15 months 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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Scholar 17 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 18 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
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Popular Question 2.0 years ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Snp Coordinates Hg19, Hg18, Hg17 Changed But Also Closest Genes Etc
Popular Question 2.0 years ago, created a question with more than 1,000 views. For SNP in Transcription factor binding site analysis
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
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Scholar 2.7 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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