User: bmpbowen

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bmpbowen40
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Posts by bmpbowen

<prev • 19 results • page 1 of 2 • next >
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Answer: A: Non-overlapping genomic haplotype blocks
... This might be helpful: "Approximately independent linkage disequilibrium blocks in human populations" by Berisa and Pickrell. They released LD blocks for AFR, ASN, and CEU populations using 1000 genomes data.    http://bioinformatics.oxfordjournals.org/content/early/2015/10/01/bioinformatics.btv54 ...
written 3.7 years ago by bmpbowen40
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Comment: C: Permutation Based Thresholds For Eqtl Analysis?
... "For each gene, adjusted P value is set to the rank of observed in the permutation list divided by X"… rank of what observed? Do you mean the gene's rank in the p value-sorted permutation list? Also, if you run say, 10 permutations, then you have ten permutation lists…so which adjusted P do you use ...
written 4.4 years ago by bmpbowen40
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Comment: C: Permutation Based Thresholds For Eqtl Analysis?
... Thanks! I ended up scrambling the index of samples for the gene expression, which I think achieved the same effect--namely, mixing which individual's genotype points to which individual's gene expression.  What if you have covariates that you need to include in your model? Would you scramble those ...
written 4.4 years ago by bmpbowen40
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Comment: C: R: remove rows by a list of rownames
... Make sure to up vote the solutions that worked for you.  ...
written 4.4 years ago by bmpbowen40
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Comment: C: Permutation Based Thresholds For Eqtl Analysis?
... I'm new to permutation analyses of eQTL data. When you suggest to scramble genotypes, is is sufficient to simply shuffle around the SNP labels, or would one have to actually shuffle around the genotypes? Meaning, if I have a matrix as follows:                     SNP1 SNP2 SNP3 Person 1     AA     ...
written 4.4 years ago by bmpbowen40
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Comment: C: R: remove rows by a list of rownames
... What about  datawithoutVF = data[-which(rownames(data) %in% remove), ] ...
written 4.4 years ago by bmpbowen40
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Answer: A: Are GWAS biased by variation in haplotype size?
... Firstly: It depends on how the genotyping array was designed. SNPs for GWAS arrays are usually selected to tag as much variation in LD with a SNP as possible. However other arrays are designed to capture as much known variation from sequence data as possible.  The HLA region is a hallmark example a ...
written 4.4 years ago by bmpbowen40
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Answer: A: R: remove rows by a list of rownames
... Haven't tested it with your data, but try using the %nin% command from the Hmisc package:   install.packages("Hmisc") library("Hmisc") datawithoutVF = data[which(rownames(data) %nin% remove), ] ...
written 4.4 years ago by bmpbowen40
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Comment: C: Tophat more multiple alignments than mapped reads?
... I sort the unmapped.bam file, then I use Bowtie2 to align the unmapped reads. How do I check if a read in unmapped_sort.bam has a corresponding mate? I ran flagstat on unmapped_sort.bam and it seems to be missing that key information. As for introns, I've read conflicting things about whether to u ...
written 4.6 years ago by bmpbowen40
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Tophat more multiple alignments than mapped reads?
... I used bam2fastx to convert the unmapped.bam output from TopHat into new fastq files. Then I re-ran Tophat with those fastq files against a bacterial genome and got the following output: Left reads:                Input:   5476828               Mapped:       656 ( 0.0% of input)             of thes ...
tophat bam samtools unmapped rna-seq written 4.6 years ago by bmpbowen40 • updated 4.6 years ago by geek_y9.7k

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