User: drkennetz

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drkennetz360
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Posts by drkennetz

<prev • 62 results • page 1 of 7 • next >
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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 4 weeks ago by drkennetz360
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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 3 months ago by drkennetz360
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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 3 months ago by drkennetz360
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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 3 months ago by drkennetz360 • updated 3 months ago by Vitis1.9k
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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 3 months ago by drkennetz360
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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 3 months ago by drkennetz360
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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 4 months ago by drkennetz360
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Comment: C: Does Cutadapt change the x,y coordinates in the fastq read name?
... Thank you! I see in the documentation that it says plainly that paired reads should always be used together (this seems like a no-brainer). Definitely a pretty bad oversight on my part. ...
written 6 months ago by drkennetz360
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Comment: C: Does Cutadapt change the x,y coordinates in the fastq read name?
... Thanks for the info, I have not done any kind of trimming so this has been good to know! Do you have any preference for adapter trimming software? ...
written 6 months ago by drkennetz360
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Does Cutadapt change the x,y coordinates in the fastq read name?
... Hi all, I have found a high presence of Illumina adapter content in a batch of samples which were sequenced on a NovaSeq. I set out to trim the adapters using cutadapt: R1: cutadapt -a GATCGGAAGAGCACGTCTGAACTCCAGTCAC -o outputR1.fastq.gz R1_001.fastq.gz R2: cutadapt -a AGATCGGAA ...
next-gen alignment written 6 months ago by drkennetz360

Latest awards to drkennetz

Rising Star 6 months ago, created 50 posts within first three months of joining.
Scholar 7 months ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to count the total aligned bases in BAM?
Supporter 7 months ago, voted at least 25 times.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to count the total aligned bases in BAM?
Scholar 8 months ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Scholar 8 months ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Teacher 8 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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