User: steve

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Posts by steve

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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 1 day ago by steve2.4k
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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 1 day ago by steve2.4k
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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 1 day ago by steve2.4k
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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 2 days ago by steve2.4k
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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 5 weeks ago by steve2.4k
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Comment: C: How to read vcf file in python?
... personally, I just use GATK `VariantsToTable` to convert it to a .tsv first. Its much easier to parse this way. Unless you wanted something from the header? Another option might to be convert to another tabular format such as .maf ...
written 5 weeks ago by steve2.4k
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Comment: C: Snakemake vs. Nextflow: strengths and weaknesses
... This sounds like something that goes against the basic premise of Nextflow. Its possible to have multiple outputs, even a dynamic amount of outputs, but they are not released from a task until the task is complete. As far as I know, `watchPath` only works for the initiation of loading items into a c ...
written 5 weeks ago by steve2.4k
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Comment: C: Automatic IGV snapshot script
... The usage of .bam files or any other format is entirely dependent on IGV. Have you tried using it with .tdf files? Let me know if it doesn't work. Though if it does not work, you would have to investigate the IGV batch script commands needed to use them, since this tool is really just a wrapper arou ...
written 3 months ago by steve2.4k
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Comment: C: Automatic IGV snapshot script
... Yes it means that you do not have the program `xvfb-run` installed on your system. It is a wrapper script that often comes bundled with your server X11 installation. Unfortunately I am not sure that I can provide a copy because from what I've seen it can be a little platform specific. For this reaso ...
written 3 months ago by steve2.4k
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Comment: C: GPU based parallel processing in genomics tools
... In addition to this, much older software that is able to utilize CPU multithreading reaches peak throughput at 8-12 CPU threads, with diminishing returns after that. So if your workload is small, you might not even see much increase in performance with more CPUs. Unless you start moving into running ...
written 4 months ago by steve2.4k

Latest awards to steve

Popular Question 15 days ago, created a question with more than 1,000 views. For Are intron mapped reads expected from RNA based reads?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Are intron mapped reads expected from RNA based reads?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For HOMER motif discovery gives inconsistent results on repeated runs
Good Question 3 months ago, asked a question that was upvoted at least 5 times. For How to tell which transcript is the canonical transcript?
Popular Question 3 months ago, created a question with more than 1,000 views. For HOMER motif discovery gives inconsistent results on repeated runs
Scholar 4 months ago, created an answer that has been accepted. For A: HOMER mergePeaks totals don't add up to peaks input
Popular Question 4 months ago, created a question with more than 1,000 views. For HOMER motif discovery gives inconsistent results on repeated runs
Scholar 5 months ago, created an answer that has been accepted. For A: HOMER mergePeaks totals don't add up to peaks input
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Appreciated 6 months ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Student 7 months ago, asked a question with at least 3 up-votes. For How to tell which transcript is the canonical transcript?
Great Question 9 months ago, created a question with more than 5,000 views. For How to tell which transcript is the canonical transcript?
Popular Question 9 months ago, created a question with more than 1,000 views. For 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 mergePeaks totals don't add up to peaks input
Popular Question 10 months ago, created a question with more than 1,000 views. For HOMER mergePeaks totals don't add up to peaks input
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Great Question 12 months ago, created a question with more than 5,000 views. For Creating chromosome karyotype plot with R and ggplot2
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
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Popular Question 19 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
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Epic Question 23 months ago, created a question with more than 10,000 views. For Creating Interactive Volcano Plots with R and Plot.ly
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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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