User: Hotz, Hans-Rudolf

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Posts by Hotz, Hans-Rudolf

<prev • 71 results • page 1 of 8 • next >
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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 11 months ago by Hotz, Hans-Rudolf380
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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 11 months ago by Hotz, Hans-Rudolf380
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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 11 months ago by Hotz, Hans-Rudolf380
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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 11 months ago by Hotz, Hans-Rudolf380
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Comment: C: Multithreading problems with qalign
... Hi Kirk I don't have an answer (yet), I am just guessing: The Octopus genome consists of many scaffolds (over 150000, most of them less than 500nt long). This might cause the problems you encounter. What happens if you just test aligning your reads against the human genome with the same parameters? ...
written 11 months ago by Hotz, Hans-Rudolf380
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Answer: A: i need to have a package for reads alignment to reference genome
... Have a look at the QuasR package...this should work on windows. Regards, Hans-Rudolf       ...
written 12 months ago by Hotz, Hans-Rudolf380
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Answer: A: Mapping Probes to a Genome
... Hi Dario Have you looked into the QuasR package (or just the Rbowtie package)? This allows you to use a 'complex aligner' without using a system call.   Regards, Hans-Rudolf   ...
written 14 months ago by Hotz, Hans-Rudolf380
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News: informal meeting of R users from the Basel area
... We are organizing an informal meeting of R users (not restricted to bioconductor users) from the Basel area for networking and discussing the possibility of future events: Wednesday, September 7th 7PM at Zic Zac Allschwil/Basel Please sign up here: http://doodle.com/poll/p98b9ciy35pvfspv Regard ...
news R written 15 months ago by Hotz, Hans-Rudolf380
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Comment: C: How to remove aberrant chromosomes from a BSgenome object?
... Hi Depending on what you want to do, subsetting might help, eg: seqinfo(BSgenome.Rnorvegicus.UCSC.rn6)[seqlevels(BSgenome.Rnorvegicus.UCSC.rn6)[1:22]] getSeq(BSgenome.Rnorvegicus.UCSC.rn6, seqlevels(BSgenome.Rnorvegicus.UCSC.rn6)[1:22])     Regards, Hans-Rudolf     ...
written 17 months ago by Hotz, Hans-Rudolf380
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Comment: C: Splicemap (in QuasR) failed while aligning 25mers
... Hi Gabriella I was asking about the preprocessReads, since this could have been the source the problem. As you did not use it, we can rule it out. IMHO, the spliced alignments in QuasR are a 'challange' . Would you mind sharing a reproducible example with me? and I will try to look deeper into it ...
written 20 months ago by Hotz, Hans-Rudolf380

Latest awards to Hotz, Hans-Rudolf

Scholar 20 months ago, created an answer that has been accepted. For A: Using a single R installation with multiple BioConductor library installations -
Scholar 2.7 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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