User: Corentin
Corentin • 230
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Posts by Corentin
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... Cheers ! I Just tried it, it was much faster and gave me the same list of rsid. ...
written 5 days ago by
Corentin • 230
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... Hi everyone,
I have a list of 150 locations (eg: "10:112834:113150") and I would like to retrieve the variants found in these locations,
This is the command I use to get the variants (*fantom_locs* contains the list of locations):
snp_db <- useEnsembl(biomart="snp", dataset="hsapiens_snp") ...
written 5 days ago by
Corentin • 230
• updated
5 days ago by
Ben_Ensembl • 930
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... You might be interested in this post:
https://biowize.wordpress.com/2014/03/04/understanding-rsem-raw-read-counts-vs-expected-counts/
> The first time I compared raw reads counts to RSEM’s expected counts, I encountered an unexpected trend: the expected counts were not slightly lower than the r ...
written 6 days ago by
Corentin • 230
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Answer:
A: Random SNPs simulation?
... Hi, you can also try Simulome, it is quite customisable.
https://github.com/price0416/Simulome
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870732/ ...
written 6 days ago by
Corentin • 230
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... blastn has an option to set a cutoff for the percentage of identity "perc_identity"
https://www.ncbi.nlm.nih.gov/books/NBK279684/
You may have to specify "-task blastn" when running your command. ...
written 16 days ago by
Corentin • 230
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... The Trinity FAQ states that having lot of transcripts is expected (I would advise you to read it if you have not already):
> Lots of transcripts is the rule rather than the exception.
https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-FAQ#ques_why_so_many_transcripts
If you are sti ...
written 25 days ago by
Corentin • 230
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... "Good enough" is subjective and depends on your experiment, your genome, your reads quality etc... But the higher the percentage of mapped read the better.
You can look in the literature and tutorials for additional steps to check and analyse your data. RNA-seq is a popular method and a lot of reso ...
written 5 months ago by
Corentin • 230
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... Hello,
From this report only it would seems that almost all your reads mapped to a very small portion of your genome.
Do not forget that rna-seq will only map to protein-coding parts of your genome which is estimated (in humans) as 2% of the genome total size. Moreover, in rna-seq the coverage depe ...
written 5 months ago by
Corentin • 230
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... If you do not care about individual genes you can create a boxplot, one for each group. It will tell you how the overall expression is different.
If you care about individual genes and you do not have a lot of them, you can create a bar plot for each. For example, you can use **geom_bar** with the ...
written 5 months ago by
Corentin • 230
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... This is an old topic but here is a list of the tool I currently use:
- Quast, probably the most used tool to get assembly statistics, such as N50, #contigs, size of the largest contig etc... http://quast.bioinf.spbau.ru/manual.html
- Busco, this is a set of manually curated othologous genes, usefu ...
written 5 months ago by
Corentin • 230
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