User: mertes

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mertes0
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Posts by mertes

<prev • 5 results • page 1 of 1 • next >
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Comment: C: Rsubread requests longread mode for shotgun RNAseq data
... Thanks for the answer! 1) Yes the samtools quick fix helped. 2) Regarding the runtime: I can still reproduce the 30h runtime on the current R version, which is compiled with a local 4.9.4 GCC library on a Scientific Linux 7.7 version. But on the stock GCC libraries and current compiled R version, ...
written 10 weeks ago by mertes0
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Comment: C: Rsubread requests longread mode for shotgun RNAseq data
... Please check my example. It contains the link to the file. And thanks in advance! ...
written 10 weeks ago by mertes0
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Rsubread requests longread mode for shotgun RNAseq data
... Dear Rsubread developers, I wanted to use the Rsubread package to count features on shotgun RNA-seq data. But when counting, it fails due too long alignments and requests the longread mode which changes runtime from 10 minutes to 30 hours and from multi core to single core! How can we overcome the ...
rsubread counting rna-seq written 10 weeks ago by mertes0 • updated 10 weeks ago by Yang Liao200
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Comment: C: Duplicated reads if 'which' has overlapping reads in ScanBamParam
... Thanks Martin! I think this helps in the future to clarify what is parsed and extracted. ...
written 8 months ago by mertes0
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Duplicated reads if 'which' has overlapping reads in ScanBamParam
... Hey all, I stumbled over the following thread again, since I misinterpreted the which argument in *scanBamParam*. https://stat.ethz.ch/pipermail/bioc-devel/2015-February/006985.html I would expect from the 'which' argument only unique reads if I use multiple ranges overlapping or not. But the w ...
rsamtools genomicalignments documentation written 8 months ago by mertes0

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