User: Richard

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Richard570
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570
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Location:
Canada
Last seen:
2 months ago
Joined:
7 years, 8 months ago
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r****************@gmail.com

Posts by Richard

<prev • 95 results • page 1 of 10 • next >
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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 4 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 4 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 4 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 6 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 6 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 6 months ago by Richard570 • updated 6 months ago by i.sudbery6.2k
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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 8 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 8 months ago by Richard570
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Comment: A: beginner snakemake scatter gather help
... Based on the tutorial page suggested above I got this far, but am now getting "SyntaxError in line 13 of Snakefile: invalid syntax" Errors. I suspect it is due to my use of quotes in the shell command. I'm not really sure I'm on the right track so please send along any suggestions. thanks RIchar ...
written 8 months ago by Richard570
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beginner snakemake scatter gather help
... Hi folks, I usually use bash scripts to get things done, and I an going to try my hand at setting up some snakemake scripts to see if I can improve some automation and tracking for some currently ad-hoc analyses. I've gone through the examples on this page: https://snakemake.readthedocs.io/en/stab ...
snakemake written 8 months ago by Richard570

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