User: guillaume.rbt

gravatar for guillaume.rbt
guillaume.rbt450
Reputation:
450
Status:
Trusted
Location:
France
Last seen:
4 days, 2 hours ago
Joined:
3 years, 8 months ago
Email:
g************@gmail.com

Posts by guillaume.rbt

<prev • 124 results • page 1 of 13 • next >
0
votes
0
answers
118
views
0
answers
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 19 days ago by guillaume.rbt450
1
vote
0
answers
81
views
0
answers
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 21 days ago by guillaume.rbt450
1
vote
0
answers
66
views
0
answers
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 27 days ago by guillaume.rbt450
0
votes
2
answers
185
views
2
answers
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 7 weeks ago by guillaume.rbt450
0
votes
2
answers
185
views
2
answers
Comment: C: output TMM normalized counts with edgeR
... Thank for your help. Could you explain me what the "pseudo.counts" are? ...
written 7 weeks ago by guillaume.rbt450
4
votes
2
answers
185
views
2
answers
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 7 weeks ago by guillaume.rbt450 • updated 7 weeks ago by James Ashmore2.5k
0
votes
1
answer
131
views
1
answers
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 9 weeks ago by guillaume.rbt450
2
votes
1
answer
131
views
1
answer
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 9 weeks ago by guillaume.rbt450 • updated 9 weeks ago by Devon Ryan81k
1
vote
3
answers
233
views
3
answers
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 9 weeks ago by guillaume.rbt450
0
votes
3
answers
233
views
3
answers
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 9 weeks ago by guillaume.rbt450

Latest awards to guillaume.rbt

Popular Question 7 weeks ago, created a question with more than 1,000 views. For using GATK IndelRealigner
Popular Question 7 weeks ago, created a question with more than 1,000 views. For download protein sequences from NCBI
Popular Question 8 weeks ago, created a question with more than 1,000 views. For download protein sequences from NCBI
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Allele count for SNPs
Centurion 3 months ago, created 100 posts.
Popular Question 4 months ago, created a question with more than 1,000 views. For download protein sequences from NCBI
Great Question 8 months ago, created a question with more than 5,000 views. For Filter genotype in multi-sample VCF file
Popular Question 8 months ago, created a question with more than 1,000 views. For download protein sequences from NCBI
Popular Question 8 months ago, created a question with more than 1,000 views. For nb spanning reads confusion in Tophat Fusion output
Voter 10 months ago, voted more than 100 times.
Scholar 13 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Scholar 15 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Allele count for SNPs
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Convert blastn to gff3
Popular Question 22 months ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file
Supporter 23 months ago, voted at least 25 times.
Scholar 24 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Allele count for SNPs
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1882 users visited in the last hour