User: Laurent Gautier

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Posts by Laurent Gautier

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Answer: A: Methylation 450k data preprocessing using Python
... Rpy2 lets you blend R and Python. You could start by encapsulating snippets of R into functions that you call from Python. For example: from rpy2.objects import r keep_this = r(""" function(mSetSqFlt, mSet) { keep <- !(featureNames(mSetSqFlt) %in% ann450k$Name[ann450k$chr %in ...
written 3.1 years ago by Laurent Gautier810
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Answer: A: Choosing Between Rpy2 Or R?
... The idea with rpy2 is to allow access to the large amount of R code available without requiring to know R. While this is working fairly well in large majority of cases (given that the ratio number-of-complains / number-of-downloads is close to zero), this is not a complete exoneration from having a ...
written 6.8 years ago by Laurent Gautier810
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Comment: C: Solid And Hiseq
... Mutations are called after the alignment is done. The number of mutations will depend on the quality and quantity of the data, the calling algorithm called, and the parameters for the algorithm (the more stringent the less false positives, but also the more true positives missed). At similar calling ...
written 7.2 years ago by Laurent Gautier810
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Comment: C: Convert Solid Xsq To Fastq Without Intermediates Files
... That's fast, and indeed probably the fastest tool. Good to have one more around. I noted that my tools had a problem with CSFASTQ (invalid CSFASQ because of copy/paste issue - we are using either FASTQ or CSFASTA here, this remained unnoticed). After correction, the Python utility in ngs_plumbing i ...
written 7.2 years ago by Laurent Gautier810
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Comment: C: Convert Solid Xsq To Fastq Without Intermediates Files
... PyTables is using its own customizations atop HDF5 (or so it did last time I tried). This is not bad in the absolute but a potential issue when you will want to create / edit XSQ files. The utilities in ngs_plumbing can convert XSQ data to FASTA-like (FASTA if ECC, or CSFASTA + QUAL) and FASTQ-like ...
written 7.2 years ago by Laurent Gautier810
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Comment: C: Convert Solid Xsq To Fastq Without Intermediates Files
... Fixes are now in the bitbucket repository and will be included with the next release (any time between now and the end of the summer). ...
written 7.2 years ago by Laurent Gautier810
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Comment: C: Convert Solid Xsq To Fastq Without Intermediates Files
... The best might be share what you are exactly doing. I have been using it to convert SR and PE data and it appeared to work. Regarding the dependency to h5py, it is really needed: XSQ is built on HDF5. ...
written 7.3 years ago by Laurent Gautier810
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Answer: A: Working Out The Number Of Introns In A Gene Given The Number Of Exons
... [This being biology there is probably a counterexample, and this will turn out to be a trick question ] I'd say it is N_{exomes} - 1. The Wikipedia page says that the 5' and 3' UTR regions are included in the two boundary exons: [edit: typos] ...
written 7.3 years ago by Laurent Gautier810
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Comment: C: Convert Solid Xsq To Fastq Without Intermediates Files
... I had a similar thought when finally finding your page on the color space (and there is already a link to it from the doc). ...
written 7.3 years ago by Laurent Gautier810
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Answer: A: Convert Solid Xsq To Fastq Without Intermediates Files
... The XSQ format is HDF5-based, and the only added need is routine to expand the bit-packed DNA and quality strings. There is at least one alternative to the conversion tools provided by Life Technologies: ngs_plumbing.xsq (although probably not tested in all situations). István's page on color-space ...
written 7.3 years ago by Laurent Gautier810

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