User: sacha

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sacha1.9k
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Location:
France
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http://dridk.me/
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dridk
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1 month, 1 week ago
Joined:
5 years ago
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s****@labsquare.org

doctor in molecular genetics
Rennes Hospital - genomics laboratory

Posts by sacha

<prev • 260 results • page 1 of 26 • next >
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concordance metrics for exome trio analysis
... I am looking for a metrics to test if mother, father and child from a trio analysis are well assigned to my vcf file. For example the metrics would check if homozygous variants are heterozygous in both parents. Do you have a metrics or a command line tool for this task ? ...
exome vcf snp written 6 weeks ago by sacha1.9k • updated 6 weeks ago by Vivek2.4k
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Answer: A: How to run dbNSFP_sort.pl to remap coordinates ?
... Hi, I just translated dbNSFP4 to hg19 using my own script without dbNSFP_sort.pl . # Copy header zcat dbNSFP4.0a_variant.chr1.gz|head -n1 > dbNSFP4_hg19.txt for file in `ls dbNSFP4.0a_variant.chr*.gz` do echo "process $file `date`" # switch column 8,9 with 1,2 ...
written 6 months ago by sacha1.9k
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Is there a benefict of denoising reads for project that are not using 16S amplicon ?
... Hi, I just discovered "denoising" method in 16S amplicon analysis (DADA2, Deblur) . If I understood, this method can infer reads sequences without errors comming from technical process . ( an error model is computed ). I wonder why we don't use this method for all projects which involved amplicon ...
illumina 16s denoising amplicon written 14 months ago by sacha1.9k • updated 14 months ago by Asaf7.2k
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How can view haplotype from GnomAD
... Hi, Is there a place to view haplotype from gnomAD ? For instance, I would like to show all variants linked to a specific variant . ...
haplotype gnomad haploview written 14 months ago by sacha1.9k
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t-rna gene symbol nomenclature
... Hi, Could you explaing the naming of t-rna gene symbol ? I have the following name : tRNA-Ala (AGC) 1-2 what is the meaning of the last two digits ? ...
gene name terminology rna written 15 months ago by sacha1.9k
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find major transcript from a specific tissue
... Hi, How can I know which transcript is majoritary used for a specific tissue ? For exemple, I would like to known for CDH1 gene, which transcript is majoritary expressed in stomach . Any database ? ...
database rna-seq written 18 months ago by sacha1.9k • updated 18 months ago by kristoffer.vittingseerup3.0k
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Comment: C: Pipeline for trusight RNA fusion kit
... Ok. But this is the first step of the pipeline. I expect something more to detect fusion gene. Thanks for the link, I will take a look. ...
written 18 months ago by sacha1.9k
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Pipeline for trusight RNA fusion kit
... Hi, Do you have any suggestion of pipeline I can use to detect fusion gene for clinical purpose ? I have data from Illumina [trusight RNA kit.][1] [1]: https://emea.illumina.com/products/by-type/clinical-research-products/trusight-rna-pan-cancer.html ...
rna-seq written 18 months ago by sacha1.9k • updated 18 months ago by Charles Warden7.6k
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Comment: C: Dna Pattern Matching In Python for Analysis
... Is the previous code the expected result? So, if you have a large dataset, you can avoid creation of matrix. This is not efficient, but will work : patterns = [] seq1 = str(next(SeqIO.parse("test.fa", "fasta")).seq) for i in range(len(seq1)): pattern = list() for ...
written 18 months ago by sacha1.9k
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Answer: A: Dna Pattern Matching In Python for Analysis
... Something like this ? #### Input fasta file : test.fa >A AAAAAAAAA >B AAAAACAAG >C GAAAACGAA >D AAAAAAAAT #### Python counter from Bio import SeqIO import pandas as pd from collections import Counter df = pd.DataFrame() for r ...
written 18 months ago by sacha1.9k

Latest awards to sacha

Popular Question 4 months ago, created a question with more than 1,000 views. For Where Can I find Chromatograms from Sanger analysis ?
Popular Question 4 months ago, created a question with more than 1,000 views. For compute count of position coverage with bedtools
Popular Question 4 months ago, created a question with more than 1,000 views. For awk filed with different separator
Popular Question 4 months ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Popular Question 5 months ago, created a question with more than 1,000 views. For Compare random and non-random mutation distribution
Student 5 months ago, asked a question with at least 3 up-votes. For What's the difference between mpileup output and bcftools call ?
Appreciated 5 months ago, created a post with more than 5 votes. For Big Browser : a new genom browser in development
Popular Question 9 months ago, created a question with more than 1,000 views. For Where Can I find Chromatograms from Sanger analysis ?
Popular Question 9 months ago, created a question with more than 1,000 views. For awk filed with different separator
Popular Question 9 months ago, created a question with more than 1,000 views. For Compare random and non-random mutation distribution
Popular Question 9 months ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Popular Question 12 months ago, created a question with more than 1,000 views. For Count repeat sequence
Popular Question 12 months ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Popular Question 13 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Popular Question 14 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Popular Question 14 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Popular Question 14 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Popular Question 14 months ago, created a question with more than 1,000 views. For Count repeat sequence
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Appreciated 17 months ago, created a post with more than 5 votes. For Big Browser : a new genom browser in development
Popular Question 17 months ago, created a question with more than 1,000 views. For Count repeat sequence
Popular Question 17 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Plotting SNP density along a chromosome from VCF files
Appreciated 18 months ago, created a post with more than 5 votes. For Big Browser : a new genom browser in development

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