User: Hotz, Hans-Rudolf

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Posts by Hotz, Hans-Rudolf

<prev • 77 results • page 1 of 8 • next >
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Comment: C: qQCReport Missing Plots Described in Documentation
... Yes, I agree the documentation is misleading (or even partly wrong). I will talk to the QuasR developers and try to get the documentation improved for of qQCReport. Hans-Rudolf ...
written 15 days ago by Hotz, Hans-Rudolf400
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Answer: A: qQCReport Missing Plots Described in Documentation
... Hi Dario The number of plots you get depends on the input, e.g. if you run qQCReport on a qproject generated from paired-end fastq files, you will get 8 plots. The plot sizes have been optimised to display several samples per page. Hope this helps/clarifies Regards, Hans-Rudolf ...
written 15 days ago by Hotz, Hans-Rudolf400
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Comment: C: Error in checkForRemoteErrors(val) : QuasR: can't pass alignment parameters
... Hi Amer Why do you want to provide "alignment parameters"? Have you read the help text for qAlign? If ‘alignmentParameter’ is ‘NULL’ (recommended), ‘qAlign’ will select default parameters that are suitable for the experiment type. Please note that for bisulfite or allele-specific ...
written 9 weeks ago by Hotz, Hans-Rudolf400
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Answer: A: EdgeR filtering, gene expression, cpm cutoff
... see page 11 in the edgeR user guide (https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf)   Regards, Hans-Rudolf ...
written 6 months ago by Hotz, Hans-Rudolf400
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Answer: A: Installing qAlign is giving me error saying Rv3.5 do not support qAlign
... Hi Fatima qAlign is part of the QuasR package (https://bioconductor.org/packages/3.8/bioc/html/QuasR.html) Hence, you should do: source("https://bioconductor.org/biocLite.R") biocLite("QuasR")     Regards, Hans-Rudolf ...
written 9 months ago by Hotz, Hans-Rudolf400
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Answer: A: QuasR error message
... Hi Tamer What is your read length? SpliceMap (the aligner used, when 'splicedAlignment= TRUE') struggles with reads shorter than 50nts, see also: https://support.bioconductor.org/p/75869/ As a workaround, I recommend to use STAR to create the BAM files outside of QuasR and then create the qproject ...
written 15 months ago by Hotz, Hans-Rudolf400
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Comment: C: How to isolate gene from a single chromosome, RNA Seq experiment, using R packag
... Use the sequence of your transgene (ie the extra chromosome) as your 'auxiliary file'. After doing the alignment, you will get an extra BAM file for your transgene. Hope this helps, Hans-Rudolf   ...
written 2.3 years ago by Hotz, Hans-Rudolf400
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Answer: A: How to isolate gene from a single chromosome, RNA Seq experiment, using R packag
... Hi Guillaume  I am struggling to understand the actual problem you have, but have a look at the 'QuasR' package (https://bioconductor.org/packages/release/bioc/html/QuasR.html). There you have the possibility to align the reads in addition to the genome to auxiliary targets (i.e. your artificial ch ...
written 2.3 years ago by Hotz, Hans-Rudolf400
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Comment: C: Multithreading problems with qalign
... sorry, I don't understand your question, now. You have said it worked (though, with a low mapping t rate) when using 'splicedAlignment=F', haven't you? ...
written 2.3 years ago by Hotz, Hans-Rudolf400
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Answer: A: Multithreading problems with qalign
... Hi Kirt with "SpliceMap" (i.e. the alignment tool used when 'splicedAlignment=T') you don't have much flexibility. I would try to align your reads against the 200 longest scaffolds firts, then allign the un-mapped reads against the next 200 and so on. Though this is probably as slow as doing the al ...
written 2.3 years ago by Hotz, Hans-Rudolf400

Latest awards to Hotz, Hans-Rudolf

Scholar 3.0 years ago, created an answer that has been accepted. For A: Using a single R installation with multiple BioConductor library installations -
Scholar 4.0 years ago, created an answer that has been accepted. For A: Using a single R installation with multiple BioConductor library installations -

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