User: Lance Parsons

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Posts by Lance Parsons

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Comment: C: DEXSeq 1.26.0 running very slowly (stuck?)
... Only for version 1.26.0 of DEXSeq. The Galaxy wrapper is here, btw: https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq. The [dexseq.R](https://github.com/galaxyproject/tools-iuc/blob/master/tools/dexseq/dexseq.R) file. The `GALAXY_THREADS` variable is what controls the threads. ...
written 9 months ago by Lance Parsons0
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Comment: C: DEXSeq 1.26.0 running very slowly (stuck?)
... OK, looking into this further, the problem comes when I enable multiple threads. It's fine as long as I only use one thread. The older version (1.24.0) worked fine with multiple threads, but isn't able to produce an HTML report (due to bugs in the conda package). So, for now I've got a workaround, b ...
written 9 months ago by Lance Parsons0
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Comment: C: DEXSeq 1.26.0 running very slowly (stuck?)
... No, at the moment I don't know. However, it does not appear to be related to the report generation, since I've tried both with and without it, and it's still not finishing in a reasonable time. I haven't had the chance to extract everything and setup a run "manually" to try and replicate this yet. J ...
written 10 months ago by Lance Parsons0
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DEXSeq 1.26.0 running very slowly (stuck?)
... I'm trying to get DEXSeq to run in Galaxy. I'm able to get the older version 1.24 to run in Galaxy, however, due to issues with the Bioconda package the generation of the HTML reports would fail. So, I updated the Bioconda package to the latest supported by Bioconda (1.26.0) and updated the DEXSeq G ...
dexseq written 10 months ago by Lance Parsons0
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Comment: C: DEXSeqHTML getListElement GRanges error
... Thanks Alejandro. I was able to work around the issue by updating the bioconductor package to DEXSeq 1.26.0. However, there are a couple of issues with the python scripts that I'd like to address. The biggest issue is on line 175 of dexseq_count.py there is a version test that fails for HTSEQ v ...
written 10 months ago by Lance Parsons0
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Comment: C: DEXSeqHTML getListElement GRanges error
... I'm making progress in resolving the issue. It seems that moving to the bioconda package for 1.26.0 fixes the problem. However, I've realized that the python helper scripts aren't compatible with python3. It's a pretty minor change to fix them, and I'd be happy to submit a PR or patch. What is your ...
written 10 months ago by Lance Parsons0
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Comment: C: DEXSeqHTML getListElement GRanges error
... Not easily, as I said this is being run via the Galaxy wrapper. The command being executed is: mkdir ./html_out && Rscript '/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/dexseq/f89c9b25feb4/dexseq/dexseq.R' -o '/galaxy/files/000/378/dataset_378056.dat' -p ${GALAXY_SLOTS:-4} -f '[["N2 ...
written 11 months ago by Lance Parsons0
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DEXSeqHTML getListElement GRanges error
... When running DEXSeqHTML, I got the following error: Fatal error: An undefined error occured, please check your input carefully and contact your administrator. converting counts to integer mode Warning message: In DESeqDataSet(rse, design, ignoreRank = TRUE) : some variables in design formula are ...
dexseq software error bug written 11 months ago by Lance Parsons0 • updated 11 months ago by nitesh.turaga140
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Gviz Alignments Track - read orientation
... When displaying individual reads in the AlignmentTrack, I can see the orientation of each read by an arrow shape, but only if I am zoomed in enough.  Once I'm zoomed out a bit, I lose that information (each read is simply a rectangle). Is there a way I can control this behavior?  Or perhaps color re ...
gviz written 4.7 years ago by Lance Parsons0 • updated 4.7 years ago by florian.hahne@novartis.com1.6k

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