User: regue.hadrien

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Posts by regue.hadrien

<prev • 33 results • page 2 of 4 • next >
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R : Plotting several variables using ggplot geombar
... Hi there, I'm currently struggling with ggplot geombar. To present quickly the data, we've computed the proportion of several virus in diferent kind of samples (column sample). 3 different protocols have been used (column proto) in triplets (column dupli). I would like to plot the proportion of e ...
R ggplot2 written 3 months ago by regue.hadrien30 • updated 3 months ago by aaragak140
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Comment: C: compute genome coverage from specific bam contig
... It worked perfectly, thx a lot:) ...
written 3 months ago by regue.hadrien30
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compute genome coverage from specific bam contig
... Hi there, I have a BAM file containing mutliple contigs. I want to compute coverage only on a specific contig. I'm usualy using bedtools for computing coverage directly on my bam, like that: bedtools genomecov -ibam simple.bam > simple.cov The problem is that when i'm using this command on ...
bedtools samtools written 3 months ago by regue.hadrien30
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Comment: A: Snakemake and BBsplit.sh for filtrate human reads : memory management
... I'm a bit late, but thanks to everyone posted here! Managing resources for snakemake seems to be a good way to limit multiple jobs. This perfectly solved my problem. ...
written 6 months ago by regue.hadrien30
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5 follow
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Snakemake and BBsplit.sh for filtrate human reads : memory management
... Hi there! I have a list of paired fastq. I want to filtrate human read from each of these pairs using BBmap tool. here is a functionnal snakemake rule i wrote: #Removing human reads from fastq rule clean_fastq: message: "Removing human reads from fastq." input: ...
bbmap snakemake written 7 months ago by regue.hadrien30
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Comment: C: Snakemake - generate an unkown file in input
... Well, you totally rigth! I didn't think about it at all. It should be more easier to handle this way with snakemake. Thanks for this advice and all of your tips on the second answer. ...
written 7 months ago by regue.hadrien30
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Comment: C: Snakemake - generate an unkown file in input
... Thx for your feedback. I'm still not very familiar with snakemake, that explain why i'm sometime using unapropriate functions etc... I'll analyze this carefully, thanks. The idea is not having 10 files per barcode, but only one file, determined by the Rscript. So it seems i've coded something I don ...
written 7 months ago by regue.hadrien30
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Comment: C: Snakemake - generate an unkown file in input
... In fact, I'm counting the most represented genotype in my dataset. So, depending on the dataset, it could be A, or B etc ..... ...
written 7 months ago by regue.hadrien30
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Snakemake - generate an unkown file in input
... Hello, It's me again for a new snakemake question! This time, I want to read a table in input using a R script, to generate a list of reads to keep. But this list may came from multiple source, (genotype in this case). I generate with my R script an output file `{barecode}_list_{genotype}.txt` . ...
R snakemake written 7 months ago by regue.hadrien30 • updated 7 months ago by russhh5.5k
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Comment: C: snakemake rule input from multiple directories and proceed them separatly
... Huge thanks for youre help and the dictionary advice! This code work: (BARCODE) = os.listdir('DATASET/') list_fastq={} for barcode in os.listdir('DATASET/'): list_fastq[barcode]=os.listdir('DATASET/'+barcode) rule all: input: merged_file = expa ...
written 7 months ago by regue.hadrien30

Latest awards to regue.hadrien

Scholar 8 weeks ago, created an answer that has been accepted. For A: snakemake : associating 2 wildcards for a specific mapping
Supporter 3 months ago, voted at least 25 times.

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