User: regue.hadrien

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Posts by regue.hadrien

<prev • 33 results • page 1 of 4 • next >
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Answer: A: snakemake : associating 2 wildcards for a specific mapping
... After few days of trying and searching, I found something: #Output bams after specifics reference mapping subtype_bam=[] for i in range(0,len(sample_list)): subtype_bam.append(result_repository + "FULL_SUBTYPED_BAM/"+subtype_list[i]+"/"+sample_list[i]+".bam") then: rule al ...
written 17 days ago by regue.hadrien30
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snakemake : associating 2 wildcards for a specific mapping
... Hi there, After reading [this snakemake documentation][1] and processing several tests, I'm unable to solve my problem. I'm working on influenza. I have an association table between sample and their matching subtype, like that: SAMPLE SUBTYPE TH3pos20191217_S96 H3N2_Perth16 S1967_S46 ...
wildcards snakemake written 20 days ago by regue.hadrien30
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Answer: A: Launch a snakefile involving multiple conda environment using an snakemake speci
... Well, I think I have solved my problem. I haven't created my .yaml files manualy, but individualy created individual environments for each tools and exported them such as: conda create -n nanofilt -c bioconda nanofilt conda activate nanofilt conda env export > env/nanofilt.yaml I t ...
written 6 weeks ago by regue.hadrien30
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Comment: C: Launch a snakefile involving multiple conda environment using an snakemake speci
... Sure, here is the full file: name: nanofilt channels: - bioconda - defaults dependencies: - _libgcc_mutex=0.1=main - biopython=1.76=py37h7b6447c_0 - blas=1.0=mkl - bzip2=1.0.8=h7b6447c_0 - ca-certificates=2020.6.24=0 - certifi=2020.6.20=py ...
written 6 weeks ago by regue.hadrien30
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Comment: C: Launch a snakefile involving multiple conda environment using an snakemake speci
... To be more precise, I'm working on a server, where snakemake is already installed. I haven't root access, so I've installed anaconda personnaly to use other bioinformatic tools. So yeah , snakemake is present in my base environment, but was installed before conda. Hope I was clear:) ...
written 6 weeks ago by regue.hadrien30
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Comment: C: Launch a snakefile involving multiple conda environment using an snakemake speci
... as mentionned on the [snakemake documentation][1] and [biostar tutorial][2] its possible to call tools from separate environments using snakemake. For exemple, NanoFilt is not installed on this computed, but the snakefile is working fine. However I dont know why my pipeline dont work when executed ...
written 6 weeks ago by regue.hadrien30
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Launch a snakefile involving multiple conda environment using an snakemake specific environment
... Hi everyone, I'm working on a snakefile involving several conda environements. As it's more simple (and avoid package troubles) to split each tools in a specific conda environment, I've separated my tools and calling them in my rules just like this: #trimming rule trimming: message: ...
environment snakemake conda written 6 weeks ago by regue.hadrien30
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Comment: C: R : Plotting several variables using ggplot geombar
... I'm not an expert with the tidy language, so I've just tried a dirty method: add a c(1,2,3......1,2,3) vector to my table, and thanks to your code, it worked perfectly! ![final plot][1] Thank you all for your awnsers! [1]: https://i.ibb.co/dK68NMR/Figure2.png ...
written 7 weeks ago by regue.hadrien30
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Comment: C: R : Plotting several variables using ggplot geombar
... Well, this is that kind of plot i'm trying to produce. Thanks! However i'm getting this: ![my results][1] I'm guessing that awefull output is caused by my variable dupli. Do you know how can I recode this variable to get 1/2/3 for each sample like you instead of SX, which the number doesn't matter ...
written 7 weeks ago by regue.hadrien30
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Comment: C: R : Plotting several variables using ggplot geombar
... Thx for the anwser! prop is the viral proportion in the triplicat. If you sum prop for each one: aggregate(subtable2$prop, list(subtable2$sampledupli), function(x) sum(x)) Group.1 x 1 HSV_S10 1 2 HSV_S17 1 3 HSV_S24 1 4 HSV_S3 1 5 ...
written 7 weeks ago by regue.hadrien30

Latest awards to regue.hadrien

Scholar 16 days ago, created an answer that has been accepted. For A: snakemake : associating 2 wildcards for a specific mapping
Supporter 7 weeks ago, voted at least 25 times.

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