User: guillaume.rbt

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guillaume.rbt240
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Posts by guillaume.rbt

<prev • 66 results • page 1 of 7 • next >
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Comment: C: Tajima's D Using SNP data ONLY
... Hi, As you said Tajima's D is computed thanks to segregating sites, so it's ok to use only SNPs information to obtain it. ...
written 18 days ago by guillaume.rbt240
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Comment: C: Extract specific fragments from SAM and count them
... Ok I understand. Indeed it's not that trivial. You have to parse the CIGAR string to know if your read is alt or ref at this position. This topic has already been discussed here : https://www.biostars.org/p/86199/ It seems that the person that have posted the question have written a script that d ...
written 18 days ago by guillaume.rbt240
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Comment: C: Extract specific fragments from SAM and count them
... maybe this information is already in your vcf file, you should look for the field "AD" (allelic depth), which should report the coverage of both alt and ref alleles ...
written 22 days ago by guillaume.rbt240
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Answer: A: Extract specific fragments from SAM and count them
... If you want to extract reads at a given position you can use samtools (ex chromosome 5 position 513931) : samtools view -b file.bam chr_5:513931-513932 > reads_position.bam with a list of positions extracted from your vcf, you could loop over it to extract each position : for i in $(ca ...
written 22 days ago by guillaume.rbt240
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Comment: C: Print rows only if number matches
... given that you have a tabulated table "table", and your list of id on column 19 : import re with open("./table", 'r') as f1: first=True last_int=0 last_line="" for line in f1: if(last_int == int(re.findall("\d+", line.split('\t')[18])[0]) ...
written 5 weeks ago by guillaume.rbt240
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Comment: C: CNV detection techniques, algorithms, applications ...
... a useful website that references ngs tools : https://omictools.com/cnv-detection3-category ...
written 5 weeks ago by guillaume.rbt240
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Answer: A: Print rows only if number matches
... Hi, I would do it in python, with your list of id in the file "list" (beware, not carefully tested) import re with open("./list", 'r') as f1: first = True last_int = 0 last_line = "" for line in f1: if(last_int == int(re.findall("\d+", line ...
written 5 weeks ago by guillaume.rbt240
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Comment: C: tajima D, nucleotide diversity and haplotype diversity
... Unfortunately I think your sample size isn't big enough to make those analysis. One individual per population isn't enough to have meaningful information on your populations. ...
written 5 weeks ago by guillaume.rbt240
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Comment: C: Convert blastn to gff3
... maybe you can find something on this post : https://www.biostars.org/p/277/ ...
written 6 weeks ago by guillaume.rbt240
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Comment: C: convert VCF into bayescan format
... thanks, Unfortunately the VCF -> PGD step isn't working, I don't know why ...
written 6 weeks ago by guillaume.rbt240

Latest awards to guillaume.rbt

Scholar 5 weeks ago, created an answer that has been accepted. For A: Allele count for SNPs
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Allele count for SNPs
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Convert blastn to gff3
Popular Question 8 months ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file
Supporter 9 months ago, voted at least 25 times.
Scholar 9 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Allele count for SNPs
Popular Question 14 months ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file
Popular Question 20 months ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file

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