User: y.hoogstrate

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y.hoogstrate440
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Posts by y.hoogstrate

<prev • 74 results • page 1 of 8 • next >
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Comment: C: User Tool Does Not Initialize
... Ooops, those comments should be replaced with CDATA tags (blame me!): ``` $output/file.txt ]]> ``` "After I fixed that, the program doesn't hang anymore, but it just doesn't start now." Does the whole Galaxy wrapper not load, or does the command not get executed? *This program is a wrapper fo ...
written 5 days ago by y.hoogstrate440
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Answer: A: Regarding splitter or merging the paired end sequencing file
... This can be a frustrating problem as the order in the file is often used to link R1 and R2 files rather than the names of the sequencing reads. The tools Sickle (low quality trimming only) and Trimmomatic are aware of this and put the reads of which the mate has been discarded in a separate file. Th ...
written 7 days ago by y.hoogstrate440
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Comment: C: User Tool Does Not Initialize
... Could you do something like: ``` ``` and see if this hangs? ...
written 7 days ago by y.hoogstrate440
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Comment: C: HELP! My HT seq table counts are in zero
... Devon's thought was right I suppose. Your BAM/SAM file was aligned to sequences named 'NW_003302556.1' etc while your GTF file contains sequences named 'supercont1.1'. These do not correspond causing HTSeq to not find reads aligned to 'supercont1.1'. ...
written 29 days ago by y.hoogstrate440
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Answer: A: Data managers tool: the content of data table disappear after restart Galaxy
... Galaxy makes clones of these loc files for each revision of each installed tool and does not write content always to the loc file directly in ./tool-data. In older versions of Galaxy it was possible to find all corresponding loc files via the web interface but this has disappeared some time ago. Any ...
written 6 weeks ago by y.hoogstrate440
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Answer: A: Data managers tool: the content of data table disappear after restart Galaxy
... This does not sound like normal Galaxy behaviour. Did you test this in planemo or in a Galaxy instance? Galaxy usually writes to flat LOC files and as far as I know there is no mechanism that automatically reverts or resets. Is the name of the loc file not used by others tools maybe? Does your file ...
written 7 weeks ago by y.hoogstrate440
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Answer: A: BAM files fail to be recognized
... Those are SAM files, not BAM files. Can you convert (revert?) them with 'SAM-to-BAM convert SAM to BAM' and see if that works out for you? ...
written 7 weeks ago by y.hoogstrate440
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Answer: A: STAR in multiple threads faces issues in opening genome file
... how much memory do you have in that machine? The Galaxy wrapper has set `--genomeLoad NoSharedMemory` (default STAR option). The consequence is that running two jobs in parallel, makes two copies of the reference genome (~30gb) in the RAM. Could this have anything to do with it? ...
written 3 months ago by y.hoogstrate440
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Answer: A: STAR in multiple threads faces issues in opening genome file
... Do you use references genomes from history or from Galaxy's cache and are you running STAR on identical or Different references? ...
written 3 months ago by y.hoogstrate440
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Comment: C: User Tool Does Not Initialize
... This is where work starts to become fun ;) ...
written 4 months ago by y.hoogstrate440

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