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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1 day, 11 hours ago
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s****@labsquare.org

doctor in molecular genetics
Rennes Hospital - genomics laboratory

Posts by sacha

<prev • 266 results • page 1 of 27 • next >
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Comment: C: How can I get the uncompressed size of a BGZIP file ?
... Ok ! I am asking because tbi is more common than gzi. So, I wonder if I can get this information from this index too. ...
written 8 weeks ago by sacha2.0k
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Comment: C: How can I get the uncompressed size of a BGZIP file ?
... Is gzi same as tbi index ? ...
written 8 weeks ago by sacha2.0k
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Answer: A: Get number of variations in a huge VCF using Tabix?
... I need to get this information from python ! Have any idea ? I guess this value should be somewhere in the file ! ...
written 8 weeks ago by sacha2.0k
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How can I get the uncompressed size of a BGZIP file ?
... Reading uncompress file size from a gzip file is easy. The value is stored in the last 4 bytes of the gzip file. But it doesn't with bgzip file ! Any idea how can I get this information without uncompress the file ? ...
bgzip binary gzip written 8 weeks ago by sacha2.0k • updated 8 weeks ago by John Marshall2.2k
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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 6 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 6 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 6 months ago by sacha2.0k • updated 6 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 11 months ago by sacha2.0k • updated 11 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 16 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 24 months ago by sacha2.0k • updated 24 months ago by Asaf8.5k

Latest awards to sacha

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