User: Hotz, Hans-Rudolf

Reputation:
390
Status:
Trusted
Location:
Switzerland
Last seen:
6 hours ago
Joined:
8 years, 3 months ago
Email:
h**@fmi.ch

Posts by Hotz, Hans-Rudolf

<prev • 72 results • page 1 of 8 • next >
0
votes
1
answers
152
views
1
answers
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 6 months ago by Hotz, Hans-Rudolf390
0
votes
2
answers
389
views
2
answers
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 18 months ago by Hotz, Hans-Rudolf390
0
votes
2
answers
389
views
2
answers
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 18 months ago by Hotz, Hans-Rudolf390
0
votes
1
answers
353
views
1
answers
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 18 months ago by Hotz, Hans-Rudolf390
0
votes
1
answers
353
views
1
answers
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 18 months ago by Hotz, Hans-Rudolf390
0
votes
1
answers
353
views
1
answers
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 18 months ago by Hotz, Hans-Rudolf390
0
votes
2
answers
295
views
2
answers
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 19 months ago by Hotz, Hans-Rudolf390
0
votes
3
answers
509
views
3
answers
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 21 months ago by Hotz, Hans-Rudolf390
0
votes
0
answers
529
views
0
answers
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 22 months ago by Hotz, Hans-Rudolf390
0
votes
1
answers
492
views
1
answers
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 2.0 years ago by Hotz, Hans-Rudolf390

Latest awards to Hotz, Hans-Rudolf

Scholar 2.3 years ago, created an answer that has been accepted. For A: Using a single R installation with multiple BioConductor library installations -
Scholar 3.2 years ago, created an answer that has been accepted. For A: Using a single R installation with multiple BioConductor library installations -

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 424 users visited in the last hour