User: sacha

gravatar for sacha
sacha1.8k
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Location:
France
Website:
http://dridk.me/
Twitter:
dridk
Last seen:
3 months, 1 week ago
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4 years, 5 months ago
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s****@labsquare.org

doctor in molecular genetics
Rennes Hospital - genomics laboratory

Posts by sacha

<prev • 258 results • page 1 of 26 • next >
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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 7 months ago by sacha1.8k • updated 7 months ago by Asaf6.1k
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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 8 months ago by sacha1.8k
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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 8 months ago by sacha1.8k
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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 11 months ago by sacha1.8k • updated 11 months ago by kristoffer.vittingseerup2.3k
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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 11 months ago by sacha1.8k
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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 11 months ago by sacha1.8k • updated 11 months ago by Charles Warden7.2k
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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 12 months ago by sacha1.8k
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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 12 months ago by sacha1.8k
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Comment: C: edit headers of fasta files
... It is a mistake. I fixed it. Sorry ...
written 12 months ago by sacha1.8k
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Answer: A: edit headers of fasta files
... I use [seqkit][1] for fasta manipulation Try to select and replace fasta header with seqkit. Use grep and replace command using regular expression and capture. Something like this : seqkit grep -nr -p "WP_\d+\.\d" test.fa|seqkit replace -p ".+(WP_\d+)\.(\d).+" -r '$1[0-9].$2' output : ...
written 12 months ago by sacha1.8k

Latest awards to sacha

Popular Question 6 months ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Popular Question 6 months ago, created a question with more than 1,000 views. For Count repeat sequence
Popular Question 7 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Popular Question 7 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Popular Question 8 months ago, created a question with more than 1,000 views. For Count repeat sequence
Appreciated 11 months ago, created a post with more than 5 votes. For Big Browser : a new genom browser in development
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Popular Question 11 months ago, created a question with more than 1,000 views. For Count repeat sequence
Popular Question 11 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Plotting SNP density along a chromosome from VCF files
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Plotting SNP density along a chromosome from VCF files
Popular Question 12 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
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Popular Question 12 months ago, created a question with more than 1,000 views. For Count repeat sequence
Scholar 12 months ago, created an answer that has been accepted. For A: bcftools extract data
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Popular Question 12 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Scholar 12 months ago, created an answer that has been accepted. For A: bcftools extract data
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Scholar 12 months ago, created an answer that has been accepted. For A: bcftools extract data
Popular Question 12 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Appreciated 12 months ago, created a post with more than 5 votes. For Big Browser : a new genom browser in development

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