User: drkennetz

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drkennetz310
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Posts by drkennetz

<prev • 46 results • page 1 of 5 • next >
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Comment: C: If a string appears twice in column 1, select the higher value in column 2
... worked like a charm! Thanks for the help. ...
written 2 days ago by drkennetz310
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If a string appears twice in column 1, select the higher value in column 2
... Hi all, I subsampled Illumina fastqs twice using 2 different random seeds. I then mapped all of the reads and got a total number of mapped reads and a mapped percent. For the same sample, I am trying to select the higher map%, as I have found for the vast majority of my samples seqtk underestimate ...
awk excel bash written 2 days ago by drkennetz310 • updated 2 days ago by cpad01127.7k
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Comment: C: Merge .bam files by groups of lanes
... I am glad to hear that! It was untested so you never know. ...
written 3 days ago by drkennetz310
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Answer: A: Merge .bam files by groups of lanes
... I think this should work for your issue: create a file name samtools_merge.sh $mkdir merged for L1 in *_L001_*.bam do echo $L1 L2=`echo $L1 | sed 's/_L001_/_L002_/'` L3=`echo $L1 | sed 's/_L001_/_L003_/'` L4=`echo $L1 | sed 's/_L001_/_L004_/'` m ...
written 3 days ago by drkennetz310
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Comment: C: Merge .bam files by groups of lanes
... This is not a job posting. The "job" tage should be used for jobs like career jobs. Most posts are about a computational "job" so I think this is implicit. Just use tags related to the type of computational job you want help with. ...
written 3 days ago by drkennetz310
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Comment: C: Realign BAM files to other reference file
... You can merge the reads if they are from the same sample and if they are the same prep (IE WES, WGS, RNASeq). Merge them before alignment, so you don't have to do it after and re-sort them. For your specific analysis, we will call it a metagenomic comparison because you are trying to see if reads ...
written 6 days ago by drkennetz310
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Answer: A: Realign BAM files to other reference file
... You don't want to realign aligned.bams, just start over from the file_1.fq and file_2.fq and repeat the same alignment process.The original fastqs wouldn't have been modified in any of these steps so just start from the beginning with the second reference. ...
written 7 days ago by drkennetz310
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Answer: A: CWL Workflow renaming outputs
... You will first need to do the recommendations above for your outputs from the workflow that tom.tubb suggested above. Second, in your tar-param.cwl, you can tell the code to name the output file to match the input filename, see the example script below: cwlVersion: v1.0 class: CommandLineT ...
written 8 days ago by drkennetz310
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Comment: C: scatter over optional argument
... Is the string you want to scatter over an output from a previous step? ...
written 10 days ago by drkennetz310
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Comment: C: scatter over optional argument
... Is there a reason you don't provide the argument? It seems like you should include it if you want to use it as an input. The error is returning that you are scattering over nothing. ...
written 10 days ago by drkennetz310

Latest awards to drkennetz

Scholar 3 days ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: How to count the total aligned bases in BAM?
Supporter 22 days ago, voted at least 25 times.
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How to count the total aligned bases in BAM?
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to count the total aligned bases in BAM?
Teacher 7 weeks 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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