User: wrf

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wrf0
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Germany
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2 years, 11 months ago
Joined:
3 years, 5 months ago
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w**@lrz.uni-muenchen.de

Posts by wrf

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Bam Files
... if that is indeed the problem, you also can regenerate the BAM index with samtools, like: samtools index mapped_reads.bam ...
written 2.9 years ago by wrf0
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Answer: A: Galaxy in Ubuntu14 can't find directory
... for Galaxy all processes are called/run as user "galaxy", so perhaps that user needs to be added to the group "users" or whoever is the owner of the programs. ...
written 2.9 years ago by wrf0
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Comment: C: looking for way to search through tracks for genes in Trackster
... this should work for our purposes, thanks. ...
written 3.1 years ago by wrf0
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looking for way to search through tracks for genes in Trackster
... Hello, Is there some way to search through the tracks/contigs for a gene in Trackster? Or alternatively, is there some easy way to search through gtf or gff files outside of trackster that does not involve the user downloading the files? I imagine something like a "jump to gene" or "jump to contig ...
trackster visualization written 3.1 years ago by wrf0 • updated 3.1 years ago by Jennifer Hillman Jackson25k
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data missing from visualized tracks
... Hello, I was browsing through my contigs, and I was looking for incongruities between different tracks when I noticed that there were some unlikely cases where entire tracks were missing from some contigs. Certain tracks were stating "no data for this chrom/contig" when I could search in the origi ...
trackster visualization written 3.2 years ago by wrf0 • updated 3.2 years ago by Jennifer Hillman Jackson25k
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Answer: A: How do I combine multiple SE libraries in a single Trinity run?
... not sure what you mean by SE libraries, but if these are both read pairs, then you can just concatenate the files, left with left, right with right. The paired information is in the read header (should end in /1 or /2) so it shouldn't matter if they are different libraries. ...
written 3.2 years ago by wrf0
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visualization cannot find binaries in normal galaxy path
... Hello, I am trying to configure trackster, however I keep getting errors about binaries not being found "command not found" when they are in the PATH for the galaxy user. All I can think of is that the temporary scripts from job_working_directory are generated without the PATH of the galaxy user ( ...
visualization path written 3.2 years ago by wrf0 • updated 3.2 years ago by Hotz, Hans-Rudolf1.8k
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variable slot configuration for GALAXY_SLOTS
... I am trying to configure the job_conf for our system. Our cluster is currently set up with SLURM, though this is not integrated with galaxy yet, so galaxy is just running on 16 cpus on one of the nodes. I would like to have all single processes run on the 16 cpus of the galaxy node and all other p ...
multiprocess written 3.2 years ago by wrf0 • updated 3.2 years ago by jmchilton1.1k
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Comment: C: galaxy crashes trying to load pbs-python, possibly related to visualization
... That was indeed the problem. Thanks! ...
written 3.2 years ago by wrf0
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Comment: C: galaxy crashes trying to load pbs-python, possibly related to visualization
... we are using SLURM on a gentoo system, so I'm not sure that PBS was ever configured in the first place as it is incompatible with SLURM. What would I disable to stop it from trying to load PBS? ...
written 3.2 years ago by wrf0

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