User: drkennetz

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drkennetz500
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Posts by drkennetz

<prev • 75 results • page 2 of 8 • next >
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Comment: C: Installing and importing viennaRNA to python in windows
... From the github it looks like a C program, so it doesn't make any sense to install it in python. I have only looked through a few of the directories but I don't see any python at all. ...
written 13 months ago by drkennetz500
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Comment: C: Add an item from input to an output array in CWL
... The merge_flattened is actually something I found on another one of your posts that ended up solving my problems: https://www.biostars.org/p/262337/ Super helpful for me! ...
written 14 months ago by drkennetz500
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Add an item from input to an output array in CWL
... Hi all, I have a cwl workflow where step1 outputs an array of items file. In step 2 I would like to add a file or an array of files to the array that is output from step1. Here is my example workflow: cwlVersion: v1.0 class: Workflow requirements: - class: ScatterFeatureRe ...
cwl written 14 months ago by drkennetz500 • updated 14 months ago by Michael R. Crusoe1.8k
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Comment: C: How to count the total aligned bases in BAM?
... Hi DNAngel, it does not return the per base output, but one option I would recommend for such a calculation is [sambamba depth][1]. This will return the per base output at each, although the files become quite large. [1]: https://github.com/biod/sambamba/wiki/%5Bsambamba-depth%5D-documentation ...
written 20 months ago by drkennetz500
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Comment: C: Depth of Coverage without Read Overlap
... Thank you for this! It is definitely something I will look into. I'll accept this if I find documentation similar for depth, or figure out how to do the same type of analysis using mpileup. ...
written 22 months ago by drkennetz500
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Comment: C: Depth of Coverage without Read Overlap
... I appreciate that, but I am not looking to modify the reads or generate new data, I think this can be done using bam header information but I am not sure just how. ...
written 22 months ago by drkennetz500
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Depth of Coverage without Read Overlap
... Hi guys, thanks in advance for help. I currently calculate the on target depth of coverage for a sample by using samtools depth: samtools depth -a -b bedfile.bed dupmrked_sorted_bamfile.bam > output_bamdepth.txt This outputs all bases' depth (even those with 0 coverage) within the regions ...
next-gen written 22 months ago by drkennetz500 • updated 22 months ago by Vitis2.4k
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Answer: A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
... To update this thread, sambamba depth is a wonderful library that supports multithreading which drastically increases speed but provides the same functionality as samtools depth. I would recommend everybody check out this package! [Sambamba][1] [1]: https://github.com/biod/sambamba ...
written 23 months ago by drkennetz500
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Comment: C: best practice for renaming file in CWL workflow
... I have been working with IBM quite a bit on bug fixes in regards to what they support and don't support. I work with CWLexec every day in our lab to develop pipeline automation. In theory, they support InlineJavascriptRequirement and ShellCommandRequirement but in practice CWLexec is quite picky. If ...
written 23 months ago by drkennetz500
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Comment: C: best practice for renaming file in CWL workflow
... I think either method would be acceptable and could come with their own benefits/pitfalls. For example, one benefit of using an intermediate renaming step is that it would be compatible with a greater number of execution engines such as Cromwell, cwlexec, snakemake etc.. By creating an intermediate ...
written 23 months ago by drkennetz500

Latest awards to drkennetz

Scholar 12 weeks ago, created an answer that has been accepted. For A: CommandLineTool doesn't finish
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: CommandLineTool doesn't finish
Appreciated 12 months ago, created a post with more than 5 votes. For A: How to count the total aligned bases in BAM?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How to count the total aligned bases in BAM?
Rising Star 2.1 years ago, created 50 posts within first three months of joining.
Scholar 2.2 years ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: How to count the total aligned bases in BAM?
Supporter 2.2 years ago, voted at least 25 times.
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: How to count the total aligned bases in BAM?
Scholar 2.3 years ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Scholar 2.3 years ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: How to count the total aligned bases in BAM?

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