User: bruce.moran

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bruce.moran860
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Posts by bruce.moran

<prev • 158 results • page 1 of 16 • next >
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Comment: C: Nextflow using existing Conda Environments
... Check `singularity --version`, then update your Singularity version=D N.B. the code chunk in my example needs to be saved entirely into a `recipe.container_name` file, then you can use `singularity build container_name.sif recipe.container_name` to build it and push to `https://cloud.sylabs.io/libr ...
written 3 months ago by bruce.moran860
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Comment: C: Nextflow using existing Conda Environments
... Based on a Github repo with `my_env.yaml` therein; environment section is called every time the container executes, so that is activating the env; you can pull the `centos7_conda` container to see what's in there, just installs `miniconda`, used to install that in 'project' containers but more effic ...
written 4 months ago by bruce.moran860
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Comment: C: Nextflow using existing Conda Environments
... Maybe you saw [this Github issue][1]? If I want to use conda as per your example, because the HPC I am on uses Modules, I need to: `module load conda`, then initialise: `conda init bash` and then reload the shell: `exec bash` (this gets a `(base) bmoran@cluster:$ ` prompt). Then I can specify as yo ...
written 4 months ago by bruce.moran860
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Comment: C: How to increase RAM for R scripts run in computer cluster
... https://stackoverflow.com/questions/12582793/limiting-memory-usage-in-r-under-linux Apologies, copy/pasted wrong link from bookmarks; TLDR set `ulimit` globally ...
written 4 months ago by bruce.moran860
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Comment: C: Empty network file with ARACNe-AP
... I'd start by reading [the original ARACNe paper][1] The basic premise is that genes act in networks, but defining the network is not as simple as geneA correlates with genesB, C and D, and therefore regulates them. ARACNe looks for direct pairwise interaction (e.g. between geneA+B, geneB+C, etc.) ...
written 4 months ago by bruce.moran860
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Comment: C: RNA Seq Analysis:Feature Counts are zero
... Could do *de novo*, presume this is human if swabs (buccal?), if so I'd be more inclined to see what the issue was with the data. What level of rRNA reads were in the samples? Was it polyA selection kit or rRNA depletion? Still interested in the duplication rate, think ruling out low complexity l ...
written 4 months ago by bruce.moran860
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Comment: A: Empty network file with ARACNe-AP
... Presume you have genes in the tf file that are also in the expression matrix and expressed? What's in `outputFolder` after your `calculateThreshold`? If you want to share files I can see if it runs here? ...
written 4 months ago by bruce.moran860
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Comment: C: RNA Seq Analysis:Feature Counts are zero
... I'd really want to know how long after swabs were collected was RNA extracted, what was the swab stored in (RNAlater, buffer from extraction kit)? What library kit was used? Previously might have said to look into rRNA contamination if an rRNA-depletion method was used, but nearly always polyA-sel ...
written 4 months ago by bruce.moran860
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Comment: C: Empty network file with ARACNe-AP
... I think the tf file has to have the same header as the first column of the expression matrix, so: echo "gene" > test/my_data/small_subset_new_tf.txt cat test/my_data/small_subset_tf.txt >> test/my_data/small_subset_new_tf.txt ...
written 4 months ago by bruce.moran860
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Comment: C: RNA Seq Analysis:Feature Counts are zero
... What's the experimental design here? What material are samples from? Did you do the labwork, or can you get RNA integrity/RINs? What were duplicate rates like? What are levels of CXCL1, 3, 5 like? ...
written 4 months ago by bruce.moran860

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