User: regue.hadrien

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Posts by regue.hadrien

<prev • 36 results • page 1 of 4 • next >
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samtools mpileup quality filtering for long read ONT data
... Hello there, To present brievly the plot, we're comparing consensus sequences at several base frequencies, generated by both illumina sequencing and long reads ONT. To do so, we've aligned our fastq on the reference (a linearized hepatitis B virus genome). The next step is to use the **samtools m ...
samtools long reads ont written 10 weeks ago by regue.hadrien30
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Answer: A: coverage differences between samtools depth and samtools mpileup
... thanks to your link and command, i tried: samtools mpileup -d 200000 -Q 0 --ff 2176 -f reference.fasta barcode.bam > pileup.vcf However still cant explain the depth differences, even without theses reads. Such as the position 30: P3_GTE 30 127061 DEPTH P3_GTE 30 G 142976 MPILEUP M ...
written 11 weeks ago by regue.hadrien30
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coverage differences between samtools depth and samtools mpileup
... Hello there, We're working on ONT long reads data. To check base frequencies on specific positions, we planned to use the mpileup function from samtools. We've also computed depth using samtools depth: samtools mpileup -d 200000 -Q 0 -f reference barcode.bam > barcode_mpileup.vcf samto ...
long read samtools ont written 11 weeks ago by regue.hadrien30
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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 5 months 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 5 months 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 months 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 months 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 months 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 months 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 months ago by regue.hadrien30

Latest awards to regue.hadrien

Scholar 5 months ago, created an answer that has been accepted. For A: snakemake : associating 2 wildcards for a specific mapping
Supporter 6 months ago, voted at least 25 times.

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