User: sacha

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sacha2.0k
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France
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http://dridk.me/
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dridk
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2 months, 2 weeks ago
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5 years, 7 months ago
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s****@labsquare.org

doctor in molecular genetics
Rennes Hospital - genomics laboratory

Posts by sacha

<prev • 263 results • page 1 of 27 • next >
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Answer: A: Extract reads with variant at given position
... For a specific variant, you can use [bamql][1] For instance, if you want to extract all reads from a bam file : - which support the alternate 'A' in snp : chr17:29827429 G>A bamql -f yourfile.bam 'chr(17) & nt_exact(29827429,A)' -o A.bam - which support the reference 'G' i ...
written 3 months ago by sacha2.0k
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Comment: C: Call alternative base for each position in a bam file
... I tried pysamstats by the past . I was thinking it is only for read depths . ...
written 3 months ago by sacha2.0k
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Call alternative base for each position in a bam file
... Hi, From a bam file and a target bed file, I would like to extract each base count. I don't want to skip low frequency variant and sequencing errors. It seems I cannot do this using GATK or freebayes. For instance, I would like to extract same data from IGV , even if I have a small allele frequen ...
calling bam written 3 months ago by sacha2.0k • updated 3 months ago by dariober11k
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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 8 months ago by sacha2.0k • updated 8 months 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 12 months ago by sacha2.0k
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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 21 months ago by sacha2.0k • updated 21 months ago by Asaf8.4k
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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 21 months ago by sacha2.0k
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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 22 months ago by sacha2.0k
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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 2.1 years ago by sacha2.0k • updated 2.1 years ago by kristoffer.vittingseerup3.4k
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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 2.1 years ago by sacha2.0k

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