User: darbinator
darbinator • 20
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Posts by darbinator
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... Firstly, do an analysis with GEO2R is that a good idea ? lol ...
written 13 days ago by
darbinator • 20
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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 14 days ago by
darbinator • 20
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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 4 weeks ago by
darbinator • 20
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7 days 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 5 months ago by
darbinator • 20
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5 months ago by
toralmanvar • 720
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... I will try, thank you
It's only via web interface or it can use on commande-line ? ...
written 5 months ago by
darbinator • 20
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... Hello
As part of my bioinformatic internship, one of my objectif is to perform functional annotation on single cell sequencing data, but I'm a little lost ..
Till now, I have assembly my reads (from differents SAGs) into contigs with SPADes (after doing quality control), I have use Prodigal to pre ...
written 5 months ago by
darbinator • 20
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3 months ago by
WouterDeCoster ♦ 35k
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... Bacterial genomes (is that why I chose to conserve metagenome contigs that align over 95% of my SAGs contigs, in order to work on the same lineage) ...
written 5 months ago by
darbinator • 20
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... It's a DNA data-set, cells of interests have been isolated,and after a whole genome amplification the amplified DNA obtained was sequenced in order to obtain SAGs (Single amplified genomes)
To evaluate the quality of these genomes, I used the software checkm which provides robust estimates of geno ...
written 5 months ago by
darbinator • 20
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... Hello
I'm a beginner in bioinformatic and I have to improve pretty bad single cells data (~10/20% of coverage against the genome reference of the species in question ..)
To improve these datas, i follow this workflow: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4749706/, which consists of using m ...
written 5 months ago by
darbinator • 20
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