User: drkennetz

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drkennetz440
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Posts by drkennetz

<prev • 67 results • page 2 of 7 • next >
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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 13 months ago by drkennetz440
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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 13 months ago by drkennetz440
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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 16 months ago by drkennetz440
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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 16 months ago by drkennetz440
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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 16 months ago by drkennetz440
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Comment: C: Are CWL CommandLineTool arguments guaranteed to be contiguous?
... Okay, that sounds weird to me since -1 implies the last element in a list (and the command line is a list of arguments/inputs). Either way see below, by forcing the position using `inputBinding: position` you guarantee their order. ...
written 16 months ago by drkennetz440
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Comment: C: Are CWL CommandLineTool arguments guaranteed to be contiguous?
... -1 put a at the front? ...
written 16 months ago by drkennetz440
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Answer: A: Are CWL CommandLineTool arguments guaranteed to be contiguous?
... This can be solved by giving everything an inputBinding: position:. Doing this will ensure the behavior you are looking for. For example, if you want your arguments to appear first and your inputs to appear second you can do the following: cwlVersion: v1.0 class: CommandLineTool require ...
written 16 months ago by drkennetz440
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Answer: A: How to create a list of the barcodes located in the read headers of demultiplexe
... When you say a list my mind is immediately going to python but you haven't tagged it so I will give an awk solution for you: zcat file.fastq.gz | awk 'NR == 1 || NR % 4 == 0 ' | awk -F ':' '{print $12} Your fastq is a little weird in the header line, but This will print the first line, and ev ...
written 16 months ago by drkennetz440
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Answer: A: bedtools bamtobed of mixed paired-end and non-paired datasets
... Hi tassa, samtools view -F 0x40 -h merged.bam > R1_from_merged.sam samtools view -F 0x80 -h merged.bam > R2.sam_from_merged samtools view -S -b R1.sam > R1_from_merged.bam samtools view -S -b R2.sam > R2_from_merged.bam I think you could do the -b flag in the first step ...
written 16 months ago by drkennetz440

Latest awards to drkennetz

Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: CommandLineTool doesn't finish
Appreciated 3 months ago, created a post with more than 5 votes. 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?
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Teacher 16 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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Teacher 18 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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Scholar 18 months ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
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