User: regue.hadrien
regue.hadrien • 30
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Posts by regue.hadrien
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2
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... 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.hadrien • 30
2
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1
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119
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1
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... 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 ...
written 20 days ago by
regue.hadrien • 30
0
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... 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.hadrien • 30
0
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1
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... 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.hadrien • 30
0
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1
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... 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.hadrien • 30
0
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1
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204
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... 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.hadrien • 30
0
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1
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204
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1
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... 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:
...
written 6 weeks ago by
regue.hadrien • 30
0
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1
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145
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... 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.hadrien • 30
0
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1
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... 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.hadrien • 30
0
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1
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145
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1
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... 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.hadrien • 30
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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