User: jinzheng9406

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Posts by jinzheng9406

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What is the distribution of coalescent time like?
... Hi, If I calculate the coalescent time of all sites(alleles or genes) along two chromosomes from the same human population (e.g. YRI or CEU), what is the distribution of coalescent time like ? What time do the most coalescent events occur? ( Among 50 kya ~ 100 kya ?) Could someone give me answer ...
gene coalescent coalescent time snp written 11 days ago by jinzheng94060
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Comment: C: PSMC with option -d
... TMRCA = Time of most recent common ancestor. PSMC = pairwise sequentially Markovian coalescent, a software developed by Heng Li DC is a line name in the PSMC output file. ...
written 18 days ago by jinzheng94060
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PSMC with option -d
... Hi! I want to get the local TMRCA for each locus from PSMC, so I use -d option. Could anyone tell me, which column is the local TMRCA from output file DC line? Thank you so much! ...
software error psmc written 19 days ago by jinzheng94060
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Comment: C: How to get a fake diploid sequence(each one from a population)
... Thank you. My BAMs have the @RG tags, that's mean, if I input two BAMs one time, it can get the haploid sequence for each one? ...
written 3 months ago by jinzheng94060
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How to get a fake diploid sequence(each one from a population)
... I want to use PSMC to analysis the division time of two closely human population. For that, I need to construct a pseudo-diploid sequence. Now, I have these two human populations' bam file. How should I do? Could I directly use below command? *samtools mpileup -C50 -uf | bcftools view -c - | ...
genome alignment sequence snp written 3 months ago by jinzheng94060
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An error when I used vcfutils vcf2fq
... I try to use vcfutils convert a vcf file which have been process by bcftools view. But when I run the commond 'vcfutils vcf2fq xxx.vcf > xxx.fq', there is a error. substr outside of string at /usr/local/bin/vcfutils.pl line 557, <> line 81277. Use of uninitialized value in lc at /usr/loc ...
software error genome fq written 7 months ago by jinzheng94060
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How to use samtools/bcftoos/vcfutils to call SNP
... I want to analysis a genome with PSMC After that, I want to use samtools/bcftools/vcfutils to process the data. And I want to follow these five rules: (i) that read depth wasbetween 1/3 and 2-times the average coverage; (ii) that root-mean-squared mapping quality for all analyzed sites was above ...
genome snp written 7 months ago by jinzheng94060 • updated 7 months ago by Samarth Kulshrestha140

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