User: steve

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steve2.6k
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Posts by steve

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Comment: C: CWL: how to set default values
... > I would suggest that they generate YAML formatted input templates instead of JSON few languages and frameworks which I have used have support for writing YAML out of the box, thus leading to the constant requirements for including YAML library dependencies in your software stack. On the other ...
written 5 weeks ago by steve2.6k
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Answer: A: How much RAM / how many CPUs should I allocate for Mutect2?
... MuTect2 has historically not run multi-threaded, in fact you are discouraged from enabling multithread options with it (some GATK engine multithread options were still accessible but did not work). Yes, it is excruciatingly slow to run. For memory, I only ever used [12GB](https://github.com/NYU-Mole ...
written 6 weeks ago by steve2.6k
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Comment: C: Which programming langauge shall I start as a beginner in Bioinformatics
... if you care about your end-user's happiness and sanity, then stay away from any language that requires an interpreter or runtime. Managing Python and R libraries is by far one of the worst things about working in Bioinformatics. And containers do not make it much better, just means you now need to t ...
written 9 weeks ago by steve2.6k
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Comment: C: A free temporary HPC service for bioinformatic analysis
... I remember a long time ago looking into [TACC](https://www.tacc.utexas.edu/use-tacc/getting-started;jsessionid=ADDBD382B6989BDD6620AD27BAAF8711) and [XSEDE](https://portal.xsede.org/#/guest) for HPC resource but never got around to using them; not sure they have a free tier still, I remember having ...
written 3 months ago by steve2.6k
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Comment: C: Editing tools script in a docker container
... you either re-build the Singularity container from the recipe (Dockerfile or Singularity file) with the changes you like or, preferably, do not use hard-coded locations to write files to, you should be using the volume bind flags to bind in locations on the host system and direct the container to r ...
written 4 months ago by steve2.6k
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Answer: A: Pindel installation failing due to htslib
... Try this: FROM ubuntu:16.04 RUN apt-get update && \ apt-get install -y wget \ bzip2 RUN wget https://repo.continuum.io/miniconda/Miniconda3-4.4.10-Linux-x86_64.sh && \ bash Miniconda3-4.4.10-Linux-x86_64.sh -b -p /conda && \ rm -f Minico ...
written 4 months ago by steve2.6k
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Comment: C: methplotlib: visualization and analysis of modified nucleotides from nanopore se
... I think the name will help it attract more attention ...
written 4 months ago by steve2.6k
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Comment: C: Copying BCL files from BaseSpace directly into tar.gz
... yeah in the past I have just used `basemount` to keep the BaseSpace location mounted to the server I am on, then you can implement your automatic methods however you want. https://basemount.basespace.illumina.com/ If you already have an AWS instance then maybe you can just mount it there? Not sure ...
written 4 months ago by steve2.6k
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Tutorial: How to run CWL with Nextflow
... *And you may find yourself with a bunch of CWL's* *And you may find yourself wanting to use a Nextflow feature* *And you may ask yourself, well How did I get here?* ----- As the debate between CWL and Nextflow rages on, and the [efforts to make them cross-compatible](https://github.com/nextflow- ...
tutorial cwl nextflow written 4 months ago by steve2.6k
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Comment: C: How to read vcf file in python?
... also it sounds like your installation of `pyvcf` is messed up. I would consider trying the version in `conda`; https://anaconda.org/bioconda/pyvcf ...
written 6 months ago by steve2.6k

Latest awards to steve

Appreciated 6 weeks ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Appreciated 3 months ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Popular Question 3 months ago, created a question with more than 1,000 views. For Are intron mapped reads expected from RNA based reads?
Appreciated 3 months ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Popular Question 5 months ago, created a question with more than 1,000 views. For Are intron mapped reads expected from RNA based reads?
Popular Question 6 months ago, created a question with more than 1,000 views. For Are intron mapped reads expected from RNA based reads?
Popular Question 7 months ago, created a question with more than 1,000 views. For HOMER motif discovery gives inconsistent results on repeated runs
Good Question 8 months ago, asked a question that was upvoted at least 5 times. For How to tell which transcript is the canonical transcript?
Popular Question 8 months ago, created a question with more than 1,000 views. For HOMER motif discovery gives inconsistent results on repeated runs
Scholar 9 months ago, created an answer that has been accepted. For A: HOMER mergePeaks totals don't add up to peaks input
Popular Question 9 months ago, created a question with more than 1,000 views. For HOMER motif discovery gives inconsistent results on repeated runs
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Scholar 10 months ago, created an answer that has been accepted. For A: HOMER mergePeaks totals don't add up to peaks input
Appreciated 11 months ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Student 12 months ago, asked a question with at least 3 up-votes. For How to tell which transcript is the canonical transcript?
Great Question 14 months ago, created a question with more than 5,000 views. For How to tell which transcript is the canonical transcript?
Popular Question 14 months ago, created a question with more than 1,000 views. For HOMER mergePeaks totals don't add up to peaks input
Popular Question 14 months ago, created a question with more than 1,000 views. For HOMER mergePeaks totals don't add up to peaks input
Popular Question 15 months ago, created a question with more than 1,000 views. For HOMER mergePeaks totals don't add up to peaks input
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Great Question 17 months ago, created a question with more than 5,000 views. For Creating chromosome karyotype plot with R and ggplot2
Popular Question 20 months ago, created a question with more than 1,000 views. For HOMER mergePeaks totals don't add up to peaks input
Popular Question 23 months ago, created a question with more than 1,000 views. For HOMER mergePeaks totals don't add up to peaks input

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