User: dragon28

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dragon2830
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Posts by dragon28

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Answer: A: Flow issues? (no temp SAM/BAM to start run?)
... Great! Thank! Hope you can help with the resources available. ...
written 11 months ago by dragon2830
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Answer: A: Flow issues? (no temp SAM/BAM to start run?)
... Hi Jennifer, I just have two pairs of files (2x LAA and 2x LV). That is all which is being used for the inputs. The error is coming about as a result of trying to run the workflow; no error messages are being shown in the history (doesn't get that far). workflow-->diff1-->run-->choose f ...
written 11 months ago by dragon2830
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Answer: A: Flow issues? (no temp SAM/BAM to start run?)
... Hi All, Just re-ran and the problem persists (nothing changed; still unable to run workflow). I waited some time for things to settle after the system changes. Any idea to to overcome? Mike p.s. oddly, my prior message about the workflow disappeared. here is the workflow: https://usegalaxy.o ...
written 11 months ago by dragon2830
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Comment: A: Flow issues? (no temp SAM/BAM to start run?)
... Hi Jennifer, Just tried and the problem persists. Seems similar with the issues raised by Bao. My workflow is NOT top secret :) and may be found here: https://usegalaxy.org/u/mike-2/w/diff1 Thanks for investigating! Mike ...
written 12 months ago by dragon2830
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Flow issues? (no temp SAM/BAM to start run?)
... Hi, Trying to run a workflow. But cannot due to the insistence of cuffdiff on existence of SAM/BAM file(s) (which are not generated before the workflow is run). This really seems to limit the utility of workflows. Is there any way to get past this (p.s. in prior runs of this workflow, this was no ...
bam samtools usegalaxy.org workflow written 12 months ago by dragon2830
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Job execution delays/issues at Galaxy Main (http://usegalaxy.org). Tophat and others. Update link included.
... Hi, Tophat is continually running for days. Sometimes it does not work and produces a vague message (last time: An error occurred with this dataset). Perhaps not a perfect dataset, but should be able to complete a run. Should I strive to use trimgalore to get as high a quality score prior to runn ...
usegalaxy.org jobs error written 12 months ago by dragon2830 • updated 12 months ago by Jennifer Hillman Jackson23k
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Answer: A: Are DIY algorithms possible? Any shell?
... Hi Bjoern, Yes, what I meant by that statement was that all operations in usegalaxy.org are done manually by making selections manually, making decisions about results and manually taking action. Thanks for the quick pointer and tutorial on jupyter/ipython! Thanks again, Mike ...
written 12 months ago by dragon2830
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How to incorporate quantile normalization within a pipeline?
... Hi Biostars, How to perform quantile normalization in a pipeline on biostars? Is this done by cuffquant then cuffnorm? Or is this done automatically (eg. by cuffdiff)? Thanks in advance ...
galaxy cufflinks tophat rna-seq written 12 months ago by dragon2830 • updated 12 months ago by Jennifer Hillman Jackson23k
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Are DIY algorithms possible? Any shell?
... Hi Biostars, Is there any way (bash/python/C/etc.) to implement algorithms on my data in usegalaxy.org? For example, I import a fastq file, then do a QC on it and find some justification to trim it a bit. Currently, it seems it is only possible to do this manually on usegalaxy.org. In, fact it ...
ipython galaxy jupyter notebook rna-seq written 12 months ago by dragon2830

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