User: Lds

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Lds380
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4 years, 7 months ago
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Posts by Lds

<prev • 24 results • page 1 of 3 • next >
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Searching Snp Or Genotype Of A Particular Publication From Dbsnp
... Hi fellows, I'm now looking for the variants files from a published CELL paper entitled "Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers". It is said that all the SNP data are available via dbSNP, but I don't know how to fetch all th ...
dbsnp written 5.6 years ago by Lds380 • updated 5.6 years ago by Julien Textoris430
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Epo Pipeline, From Genome Fasta Files To Multiple Genome Alignment Output
... Hi fellow, I'm just wondering if I have reference genomes for 5 species, how to use the EPO pipeline in ensembl to do multiple alignment. I know I can download the EPO 35 eutherian or EPO 6 primates from ftp, but I still very curious about the 'de novo' multiple alignment pipeline, when I looked ...
alignment written 5.9 years ago by Lds380
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How To Fetch The Coordinates For Different Domains In Mirna Precursor.
... Hi fellows, Do you known how to fetch the coordinates for different domains in miRNA precursor, like the coordinates for stem, miR, miR*, loop or seed region. Thanks in advance, I'm looking forward to your answers or suggestions. ...
domain mirna written 6.2 years ago by Lds380 • updated 4.9 years ago by Biostar ♦♦ 20
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Why 4Ne Rather Than 2Ne?
... Effect population size (Ne) is an important parameter in population genetics. The recombination rate (c) and mutation rate (u) can be extended to population scale rho and theta, respectively, by multiplied by 4N{e}, that is, rho = 4N{e}c theta = 4N{e}u As human is diploid, it supposed to multipl ...
population written 6.4 years ago by Lds380 • updated 12 months ago by Biostar ♦♦ 20
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Is It Necessary To Do Base Quality Score Recalibration Before Variants Detection In Gatk
... Hi, As it mentioned in here, the reported base quality scores (the QUAL column in BAM file) before Base Quality Score Recalibration(BQSR) are neither very accurate nor informative, After recalibration, the quality scores in the QUAL field in each read in the output BAM are more accurate and then th ...
gatk written 6.4 years ago by Lds380 • updated 6.4 years ago by Zev.Kronenberg11k
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Comment: C: Why Do We Need Markduplicates For Variants Detection In Gatk Processing Pipeline
... Thanks so much. This is the discussion in seqanswers: http://seqanswers.com/forums/showthread.php?t=6854 I think that we should using MarkDuplicates in SNP calling. ...
written 6.4 years ago by Lds380
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Why Do We Need Markduplicates For Variants Detection In Gatk Processing Pipeline?
... Hi fellows, It's said that MarkDuplicates in Picard matches all read pairs that have identical 5' coordinates and orientations and marks as duplicates all but the 'best' pair. If I have three pairs, with one of which is the 'best' pair, they're all truely from the target genome but not from sequenc ...
gatk picard markduplicates written 6.4 years ago by Lds380 • updated 6.4 years ago by Alex Paciorkowski3.3k
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The Impact Of Sequencing Error On Population Genetics Parameters
... Hi fellows, Does anyone know how to simulate the impact of sequencing error on population genetics parameters, like theta, Ne, rho ... Thanks in advance ...
population sequencing written 6.4 years ago by Lds380 • updated 6.4 years ago by lh331k
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Comment: C: Confusing Definition In Vcfv4.1: Info=<Id=Dp....>
... So if I want to extract the genotype from VCF generated by samtools, I must be very careful about the DP, I should mark the genotype as missing data for samples with DP=0. ...
written 6.5 years ago by Lds380
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Comment: C: Confusing Definition In Vcfv4.1: Info=<Id=Dp....>
... Thanks so much. You've got the point. When I add flag -D in samtools to call the variants, it keep read depth for each individual. What I get for chr1:85691 is, chr1 85691 . C T 6.26 . DP=2;AF1=1;CI95=0.3333,1;DP4=0,0,2,0;MQ=40;FQ=-28.9 GT:PL:DP:GQ 0/1:0,0,0:0:3 1/1:20,3,0:1:4 1/ ...
written 6.5 years ago by Lds380

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