User: darbinator
darbinator • 40
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Posts by darbinator
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... effectively, when I launch my script with this command " snakemake -j ", The 5 jobs start at the same time (I used to simply just execute "snakemake" before), so thank's you !
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written 2 days ago by
darbinator • 40
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... Hi !
I started using snakemake to replace my bash scripts in order to have a more "pretty" code, but I have some problems, especially to parallel my jobs.
I have this code:
FILES = [ os.path.basename(x) for x in glob.glob("Experience/*") ]
SAMPLES = list(set([ "_".join(x.split("_")[ ...
written 2 days ago by
darbinator • 40
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Comment:
C: input for rMATS
... I've tried to run rMATs with two differents length with my BAM files (-readLength 100 and -readLength 130, my raw reads have 150bp but after trimming they drop around 130) , and I Have similar but note the same results from the 2 differents runs ..
So I don't really know what read length take, I do ...
written 7 days ago by
darbinator • 40
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... Hello, I update this topic because I have another question
rLogTransofrmation is fine and I have do this with my data but does DESeq2 deal with the difference in the number of reads between samples?
Because I have 3 samples from 2 conditions, the 3 samples from the first condition have all ~ 10 0 ...
written 21 days ago by
darbinator • 40
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... Ok thank's for your answers, I will have a look on SnakeMake ...
written 27 days ago by
darbinator • 40
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... Hello,
For my internship, I write some bash scripts in order to carry out a pipeline that I could reuse for future RNA seq analyzes.
I thought that in case the pieline would really elaborate, I had to go on python
So I started to "translate" my scripts into python but I realized that I mainly ca ...
written 27 days ago by
darbinator • 40
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... Firstly, do an analysis with GEO2R is that a good idea ? lol ...
written 12 weeks ago by
darbinator • 40
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... Hello !
For a project I reanalyse data from a study (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50395) in order to perform a Differential Gene Expression Analysis between 2 conditions (3 patients vs 3 controls).
My first idea was to use the software GEO2R because data values are already ...
written 12 weeks ago by
darbinator • 40
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... Hello,
In order to find biomarkers of interest related to a disease (APS) and from two studies (one gene expression array study: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50395, and one NMR-metabolites study: https://www.ebi.ac.uk/metabolights/MTBLS356), my idea was to perform firstly a ...
written 3 months ago by
darbinator • 40
• updated
11 weeks ago by
Smandape • 60
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... Hello everyone,
To explain, I have a SAG (single amplified genome) from a bacterium of interest, I have assembly reads into contigs (with SPAdes) and then I have extract the 16s RNA sequence.
I have also several metagenomics datas (filtered reads, ~100pb, ~200 000 000 reads) from differents lakes ...
written 7 months ago by
darbinator • 40
• updated
7 months ago by
toralmanvar • 750
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