User: regue.hadrien
regue.hadrien • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- Last seen:
- 1 month ago
- Joined:
- 1 year, 7 months ago
- Email:
- r************@gmail.com
Posts by regue.hadrien
<prev
• 36 results •
page 1 of 4 •
next >
0
votes
0
answers
129
views
0
answers
... 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 ...
written 10 weeks ago by
regue.hadrien • 30
0
votes
1
answer
177
views
1
answers
... 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.hadrien • 30
0
votes
1
answer
177
views
1
answer
... 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 ...
written 11 weeks ago by
regue.hadrien • 30
2
votes
1
answer
250
views
1
answers
... 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.hadrien • 30
2
votes
1
answer
250
views
1
answer
... 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 5 months ago by
regue.hadrien • 30
0
votes
1
answer
643
views
1
answers
... 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.hadrien • 30
0
votes
1
answer
643
views
1
answers
... 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.hadrien • 30
0
votes
1
answer
643
views
1
answers
... 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.hadrien • 30
0
votes
1
answer
643
views
1
answers
... 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.hadrien • 30
0
votes
1
answer
643
views
1
answer
... 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 months ago by
regue.hadrien • 30
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.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 935 users visited in the last hour