User: drkennetz

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drkennetz440
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Posts by drkennetz

<prev • 67 results • page 1 of 7 • next >
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Answer: A: Python FASTA scripting
... You can do the following: import sys def fasta_parser(fasta): """ Iterates through fasta Args: fasta (file): fasta_file Returns: seqs (list): list of seqs headers (list): list of headers """ seqs = [] ...
written 7 weeks ago by drkennetz440
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Answer: A: How to automate bcl2fastq such that it is launched every time the run finishes o
... I wrote a more generalized shell script back in the day to do the same. It actually just runs `stat` on the directory which displays the status of a file or filesystem. I did stat rather than looking for a file because locally we transfer our data from the sequencer to an hpc filesystem and sometime ...
written 7 weeks ago by drkennetz440
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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 3 months ago by drkennetz440
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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 3 months ago by drkennetz440
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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 3 months ago by drkennetz440 • updated 3 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 10 months ago by drkennetz440
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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 12 months ago by drkennetz440
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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 12 months ago by drkennetz440
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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 12 months ago by drkennetz440 • updated 12 months ago by Vitis2.3k
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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 12 months ago by drkennetz440

Latest awards to drkennetz

Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: CommandLineTool doesn't finish
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: How to count the total aligned bases in BAM?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to count the total aligned bases in BAM?
Rising Star 15 months ago, created 50 posts within first three months of joining.
Scholar 16 months ago, created an answer that has been accepted. 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?
Supporter 16 months ago, voted at least 25 times.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How to count the total aligned bases in BAM?
Scholar 17 months ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Scholar 17 months ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Teacher 17 months 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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