User: guillaume.rbt

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guillaume.rbt450
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Posts by guillaume.rbt

<prev • 124 results • page 1 of 13 • next >
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Comment: C: coverage of the reads over coding sequence only for one gene
... You can use bedtools coverage to compute the coverage at every base of your gene, then use R to output a graph of coverage over the length of your gene. (I don't really get the "0 to 100%" part) ...
written 3 months ago by guillaume.rbt450
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Comment: C: Fasta file display and edition
... You may find your answer on one on those previous questions : https://www.biostars.org/p/273248/ https://www.biostars.org/p/2226/ https://www.biostars.org/p/105388/ https://www.biostars.org/p/76716/ ...
written 3 months ago by guillaume.rbt450
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Comment: C: Best program for population structure analyses of whole genome SNP data of many
... You can use structure for inference of genetic clustering. And I know popgenome can compute several population genetic indices. ...
written 3 months ago by guillaume.rbt450
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Comment: C: output TMM normalized counts with edgeR
... Ok great, I did think there was something with the cpm function, but I get it know. ...
written 4 months ago by guillaume.rbt450
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Comment: C: output TMM normalized counts with edgeR
... Thank for your help. Could you explain me what the "pseudo.counts" are? ...
written 4 months ago by guillaume.rbt450
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output TMM normalized counts with edgeR
... Hi all, Sorry I know that this question has been asked several times, but unfortunately I haven't been able to find the right answer, or didn't understand. I'm trying to get TMM normalized counts thanks to edgeR. I understand that I have to compute normalization factors : dgList <- calcNo ...
differential expression rna-seq written 4 months ago by guillaume.rbt450 • updated 4 months ago by James Ashmore2.5k
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Comment: C: Differential expression analysis with DEseq2 : multiple groups comparison
... Thanks for the info anf for the advice. I'm curious, what would be a more relevant design to study the interaction between temperature and watering in this case according to you? ...
written 5 months ago by guillaume.rbt450
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Differential expression analysis with DEseq2 : multiple groups comparison
... Hi all, I think this question may have been already asked before, but I have not been able to find an answer, or I did not fully understand the answers, as I'm a beginner in DE analysis. Considering the following RNAseq dataseq, imported in DEseq2 : 12 samples, with 2 conditions, and 3 replicates ...
rna-seq differential expression written 5 months ago by guillaume.rbt450 • updated 5 months ago by Devon Ryan85k
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Comment: C: Detection of SNPs
... second thought, bedtools intersect is even easier to use : echo -e "2\t2241384\t2244383" > gene_position.bed bedtools intersect -a ./your_vcf.vcf -b ./gene_position.bed > filtered_vcf.vcf ...
written 5 months ago by guillaume.rbt450
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Comment: C: Detection of SNPs
... You need to get the position of your gene to extract the SNPs. For that you can do a blast with your fasta against your genome : https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch Then with the positions you can use the --position parameters from vcftools to filter your vcf : http://vc ...
written 5 months ago by guillaume.rbt450

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