User: kirt.onthank

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Posts by kirt.onthank

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Comment: C: Multithreading problems with qalign
... What makes it work is setting clObj=makeCluster(1) and only using a single core.  The issue with slicedAlignment is simply that if it is set to T, the alignment takes an unmanageable amount of time on a single core.  When I am using more than one core the R temp directory fills up with 11.0 GB of t ...
written 3.0 years ago by kirt.onthank0
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Comment: C: Multithreading problems with qalign
... Hans-Rudolf,  Thanks so much for the help and ideas.  I will chase those down. Hypothetically, If I don't use SpliceMap, (say 'splicedAlignment=T' isn't increasing my alignment %), might there be a way around this problem? Or am I still in the same hole? Thanks again, Kirt ...
written 3.0 years ago by kirt.onthank0
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Comment: C: Multithreading problems with qalign
... Hans-Rudolf,  Thanks for the suggestion.  I aligned using the small test file (1000 reads) that failed when aligning to the Octopus genome, and instead use the Human genome.  That worked perfectly.   I am using splicedAlignment=T because I had run it before with splicedAlignment=F and came away wi ...
written 3.0 years ago by kirt.onthank0
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Multithreading problems with qalign
... I am trying to map RNA-seq reads in a fastq file to the Octopus bimaculoides genome (Obimaculoides_280.fa from Metazome) using qalign in the package QuasR.  I am running this on a Dell Optiplex 7010 with 32GB of RAM.  I am attempting to multithread the command using the following: aligned=qAlign(' ...
quasr parallel written 3.0 years ago by kirt.onthank0 • updated 3.0 years ago by Hotz, Hans-Rudolf400

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