User: J.F.Jiang

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J.F.Jiang720
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720
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Location:
China
Last seen:
2 months, 3 weeks ago
Joined:
7 years, 5 months ago
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a************@gmail.com

Posts by J.F.Jiang

<prev • 242 results • page 1 of 25 • next >
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Comment: C: Free Genetic Genealogy Software
... yhaplo use isogg 2016 as the reference. Updating to 2018 is quite confusing for me. Is there any solution or other similar tool? ...
written 3 months ago by J.F.Jiang720
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Comment: C: remove primer sequences from BAM file
... yes, -L option can handle with non-overlapped regions. ...
written 3 months ago by J.F.Jiang720
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Comment: C: remove primer sequences from BAM file
... ------->--------*-------------------------------<------------- ------------>--------------------<----------------------- Take the scenario above as consideration, if position * is always T, but C in the primer region of the second amplicon. The calling result wil ...
written 3 months ago by J.F.Jiang720 • updated 3 months ago by WouterDeCoster34k
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remove primer sequences from BAM file
... Hi all, I am dealing with amplicon data, which was obtained from multiplex PCR. Original primers can largely increase the mapping accuracy, since some amplicons are highly homologous with little difference within primer region. And since these primers may introduce FAKE SNPs when they are within ...
bam primer written 3 months ago by J.F.Jiang720
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autosomal ancestry inference
... Hi all, I am very interested in ancestry inference. 1. autosomal ancestry I've followed the tutorial from https://github.com/pcgoddard/Burchardlab_Tutorials/wiki/ADMIXTURE#popfile. However, decision on cluster information K is quite confusing. For example, there are already 12 populations among ...
gwas ancestry written 3 months ago by J.F.Jiang720 • updated 3 months ago by Kevin Blighe32k
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Simulate genotypes for SNPs, considering MAF and LD structure
... Hi all, I want to simulate genotypes of several SNPs for 10,000 samples. A Bernoulli sampling is applied to generate SNP genotypes (0/0, 0/1, 1/1) for random samples. However, this will not consier the LD structure among thse SNPs, which was obtained from 1KG dataset. Is there any tools of Gith ...
maf simulation snp genotype ld written 10 months ago by J.F.Jiang720 • updated 1 day ago by zx87545.7k
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Comment: C: extract region bam
... Thanks, Either seal.sh or cutprimers.sh is spliting the raw sequencing file based on matched primers. However, I still want to begin from bam file. ...
written 11 months ago by J.F.Jiang720
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extract region bam
... Hi all, I want to extract bam of specific amplicon to evaluate the according amplicon performance. I used to use samtools view xx.bam chr:start-end to extract the bam, however, if the two amplicon are totally overlapped, this command will return us the whole reads covering the two region. For exam ...
region bam written 11 months ago by J.F.Jiang720 • updated 11 months ago by h.mon21k
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Comment: C: pairwise calculation of relationship based on selected SNPs with MAF>0.3
... I can definitely use vcftools or directly use PLINK to convert vcf to ped, and then use PLINK to calculate IBD. However, genotypes of the samples were saved into database. If I am calculating the pairwise IBD for new 1000 samples against the database. I need to extract the genotypes from database, ...
written 11 months ago by J.F.Jiang720
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pairwise calculation of relationship based on selected SNPs with MAF>0.3
... Hi all, We are genotyping ~2000 SNP in a Panel using NGS method. We want to build a metrics to calculate the relationship for one sample against all in our database, in order to avoid taking wrong samples that are already existed in our lab. I used to use PLINK to calculate IBD score for GWAS dat ...
relationship snp written 11 months ago by J.F.Jiang720

Latest awards to J.F.Jiang

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