User: Richard

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Richard570
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Canada
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21 hours ago
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8 years, 3 months ago
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Posts by Richard

<prev • 97 results • page 1 of 10 • next >
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creating container - should it contain a workflow manager?
... Hi folks. I'm constructing a simple container that will accept a pair of fastq files and run the following tools: 1. cutadapt 2. minimap2 3. Strelka2 4. SNPEff 5. BASH / SnpSift to count up some of the SNPEff results. The container is specifically required to operate on a single pair ...
singularity snakemake nextflow written 11 days ago by Richard570 • updated 10 days ago by Jeremy Leipzig19k
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matched designed sequence in nanopore reads
... Hi folks, I have reads with a known construct from which I want to extract some subsequence. As an example, this sequence represents what I'm looking at: aaaaaaaaaaaaaaaabbbbbbbbbbbbbbccccccccccddddddddeeeeeeeeeeeeeeeeeeee where the 'a' bases are nanopore adapter sequence 'b' bases are another ...
sequence alignment written 5 months ago by Richard570 • updated 5 months ago by zubenel80
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Answer: A: multiqc change sample names
... Looks like symlinking all the initial BAM files to follow the same naming convention and re-generating the results is the safest way to get the samples to line up in the tables. ...
written 10 months ago by Richard570
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Comment: C: multiqc change sample names
... One related option would be if there was a way to edit the multiqc_sources.txt file and then re-generate the report with the edited names. Might this be possibe? ...
written 10 months ago by Richard570
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multiqc change sample names
... Hi all, I'm trying to put together a multiqc report that uses the same samples multiple times and the only differences are due to the sample and centre where the data were generated. I'm trying to organize my report so I can see the centre and sample in each label. It looks like that I can use t ...
multiqc written 10 months ago by Richard570
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Comment: C: UMI with MACS
... Probably not as even though callpeak is a separate command it still documents that MACS2 will make its own decision about which reads are duplicates. ...
written 13 months ago by Richard570
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Comment: C: UMI with MACS
... Maybe this will work if I just use the "callpeak" function. ...
written 13 months ago by Richard570
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UMI with MACS
... Hi folks. We have some ChIP data with UMIs in the reads. We are planning to duplicate mark using either umi_tools or Picard to mark duplicates in a UMI aware fashion. I see in the docs that MACS will mark duplicates in its own way: https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-usi ...
macs umi chip-seq written 13 months ago by Richard570 • updated 13 months ago by i.sudbery7.7k
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Comment: C: beginner snakemake scatter gather help
... Thanks Jeremy, For the directory command, I was hoping to create a folder to hold the smaller VCF files per sample. That way it keeps all the files for each sample separate. For example, I have the following in "input" bam1.bam bam2.bam bam3.bam For each of the bam files I wanted to create a fo ...
written 15 months ago by Richard570
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Comment: C: beginner snakemake scatter gather help
... Great! That seemed to help. Now it looks like I'm struggling to understand the wildcards. In the code below I want to process each BAM files in the folder "input/" to create 1 final VCF per BAM file. My current error is "RuleException in line 7 of /projects/rcorbettprj2/GATK4.0.10_snakemake/S ...
written 15 months ago by Richard570

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Popular Question 25 days ago, created a question with more than 1,000 views. For Affy 500K positions in hg38
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