User: correlationmatrix

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Posts by correlationmatrix

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Criteria for excluding genes from Fisher tests (presence of mutation vs sample group). Minimum number of samples mutated?
... I would like to test a number of different genes as to whether a mutation in that gene is significantly associated with a particular group of samples. Thus, for each gene I will perform a Fisher test to compare the number of samples in group A with any mutation in gene 1, vs the number of samples in ...
fisher samples mutation written 2 days ago by correlationmatrix10 • updated 2 days ago by theobroma22380
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Comment: C: How to output all variant alleles at a given site, regardless of quality
... You're right, that was the issue! ...
written 3 months ago by correlationmatrix10
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Comment: C: How to output all variant alleles at a given site, regardless of quality
... Works! Although in this case I was only interested in looking up specific regions, but subsetting the BAM file using samtools first solves the problem. However, I got some Java errors when running callvariants.sh: "Invalid maximum heap size: -Xmx101593m. The specified size exceeds the maximum repre ...
written 3 months ago by correlationmatrix10
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How to output all variant alleles at a given site, regardless of quality
... How can one use either samtools mpileup or any other tool to, for a given position, output all alternate alleles regardless of quality? Just "samtools mpileup" (and the parameters I've tried so far) gives <*> for a position for which I observe an alternate base in IGV. (The purpose of doing th ...
variant snp mpileup written 3 months ago by correlationmatrix10 • updated 3 months ago by Brian Bushnell10k
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Issues when scaling the TOM:s for consensus network construction with WGCNA
... Hi! I am attempting to perform a consensus co-expression network analysis with WGCNA based on two datasets (same experiment). Everything seems alright until I reach the step where one should scale the topological overlap matrix of dataset 2 to be comparable to the one derived from dataset 1. Speci ...
wgcna written 3 months ago by correlationmatrix10

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