User: darbinator

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darbinator40
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Posts by darbinator

<prev • 15 results • page 1 of 2 • next >
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Comment: C: How to parallelize a rule in Snakemake ?
... 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 ! ...
written 2 days ago by darbinator40
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How to parallelize a rule in Snakemake ?
... 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("_")[ ...
ngs pipeline snakemake rna-seq written 2 days ago by darbinator40
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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 darbinator40
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Comment: A: Help! How to plot RNASeq data in PCA
... 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 darbinator40
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Comment: A: Scripting a NGS analysis pipeline, in Shell or Python ?
... Ok thank's for your answers, I will have a look on SnakeMake ...
written 27 days ago by darbinator40
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Scripting a NGS analysis pipeline, in Shell or Python ?
... 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 ...
python ngs analysis rna-seq bash written 27 days ago by darbinator40
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Answer: A: Question about Differential Gene Expression Analysis with GEO2R
... Firstly, do an analysis with GEO2R is that a good idea ? lol ...
written 12 weeks ago by darbinator40
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Question about Differential Gene Expression Analysis with GEO2R
... 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 ...
gene differential expression analysis geo2r written 12 weeks ago by darbinator40
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How to integrate GSEA (genes) and MSEA (metabolites) analysis ?
... 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 ...
gene analysis metabolites rna-seq written 3 months ago by darbinator40 • updated 11 weeks ago by Smandape60
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How to have the abundance of my bacterium of interest in a metagenomic dataset
... 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 ...
gene genome next-gen written 7 months ago by darbinator40 • updated 7 months ago by toralmanvar750

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