User: drkennetz

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drkennetz370
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Posts by drkennetz

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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 5 months ago by drkennetz370
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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 7 months ago by drkennetz370
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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 7 months ago by drkennetz370
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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 7 months ago by drkennetz370 • updated 7 months ago by Vitis2.1k
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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 7 months ago by drkennetz370
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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 7 months ago by drkennetz370
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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 8 months ago by drkennetz370
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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 10 months ago by drkennetz370
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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 10 months ago by drkennetz370
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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 10 months ago by drkennetz370

Latest awards to drkennetz

Rising Star 10 months ago, created 50 posts within first three months of joining.
Scholar 11 months ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to count the total aligned bases in BAM?
Supporter 11 months ago, voted at least 25 times.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to count the total aligned bases in BAM?
Scholar 12 months ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Scholar 12 months ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Teacher 12 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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