User: Xavier Pastor

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Posts by Xavier Pastor

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Answer: A: R bioconductor in analysying methylation data
... For some reason the odds that limma::goana is calculating either give non finite values or negative values. The key line of the function could be the following: Odds <- S[, "PP"]/(SumPP - S[, "PP"]) * M2/S[, "N"] Where S[,'PP'] is the summed prior probability of all the probes for a given G ...
written 3 months ago by Xavier Pastor0
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Comment: C: cpu usage in pindel for samples aligned with bwa mem
... I'd just like to mention that after removing the supplemental reads in the bwa mem alignment (samtools view -bh -F 0x800) pindel seems to behave similar as to bwa aln alignments, at least computationally. I still need to confirm how about the final results. If this is true I guess my initial suspic ...
written 4.1 years ago by Xavier Pastor0
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cpu usage in pindel for samples aligned with bwa mem
... I’m using pindel on a set of sample pairs aligned using bwa mem but it doesn’t make a good usage of the specified threads. In addition it seems to take too long to process a single chromosome. When I run pindel on the same samples but aligned using bwa aln the profile of multithreaded usage is comp ...
next-gen pindel written 4.3 years ago by Xavier Pastor0 • updated 3.3 years ago by Biostar ♦♦ 20

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Popular Question 3.5 years ago, created a question with more than 1,000 views. For cpu usage in pindel for samples aligned with bwa mem

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