User: seta

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seta1.2k
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Posts by seta

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Merging a large number of VCF files
... Dear all, I have a previously merged VCF file per chromosome (say, 22 VCF files) containing about 1000 samples; Also, there is a large number of single sample VCF files (with all chromosomes) that should be merged with the previously merged vcf file per chromosome. Could you please suggest to me th ...
vcf merging whole genome written 5 days ago by seta1.2k • updated 5 days ago by Pierre Lindenbaum124k
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Comment: C: Gene-based common and rare variant association analysis
... Hi Kevin, Thank you for your response and introducing your package. Sorry, I read the manual of RegParallel, but it isn't sufficient for me to do the analysis as it's my first experience on this issue. I have the data in plink format, could you please kindly show me how I can test the association o ...
written 11 weeks ago by seta1.2k
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Gene-based common and rare variant association analysis
... Dear all, I’m going work on a given gene with about 170 variants derived from whole genome sequencing of a population (unrelated and related individuals). Most variants are low frequent and rare (AF < 0.05, AF<0.01); in fact there are just 14 common variants and the rest of them are rare. Al ...
skat association analysis common rare variant written 12 weeks ago by seta1.2k • updated 11 weeks ago by Kevin Blighe51k
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Comment: C: Getting a sample of 1000 random SNPs with MAF
... Hi Shicheng, I also need to make a set of random SNP with the similar allele frequency with my SNP list. Could you please let me know how did you solve the problem? ...
written 3 months ago by seta1.2k
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Window-based Fst analysis
... Hi all, I used vcftools for Fst calculation of a set of snp (about 2000) with varying window size and step, like window and step size of 50bp-5bp, 500bp-50bp, 1000bp-100bp, and 100kbp-10kbp. Obviously, the calculated Fst is different among different parameters. But, I'm not sure how I should select ...
population genetic fst written 4 months ago by seta1.2k
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Comment: C: bedtools closest return no output!
... Thanks, the files have not such a problem that you mentioned. I tried `bedtools window` and worked well. Sorry, what's the main difference between these two options, closest and window? ...
written 4 months ago by seta1.2k
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bedtools closest return no output!
... Dear all, I'm trying to get the upstream and downstream genes of a specific long non-coding RNA (lncRNA) in rat. To this end, I download the rat GTF file from Ensembl and converted to bed format by `fgrep -w gene rat.gtf | sed 's/[";]//g;' | awk '{OFS="\t"; print $1, $3, $4-4,$5,$12,0,$7,$18,$14,$1 ...
bedtools gtf nearest gene written 4 months ago by seta1.2k
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Comment: C: Convert HLA allele to Genepop format
... yes, I can use it. But, I just want to make sure this conversion is right? ...
written 4 months ago by seta1.2k
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Comment: C: Convert HLA allele to Genepop format
... Yes Kevin, I saw those links, I tried the PGDspider, but it didn't work for me. Based on the example of genepop format at [here][1], I manually changed the above format (in the original post) to the below format: Loc1, Loc2, Loc3, Loc4, Loc5 POP NA18500, 3301 7401 5801 7801 1601 NA ...
written 4 months ago by seta1.2k
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Comment: C: Recoding HLA Alleles by 01
... Hi Kevin, what about the conversion of HLA allele to popgene format; could you please take a look at [this post ][1]? do you have any suggestion? Thanks [1]: https://www.biostars.org/p/389549/ ...
written 4 months ago by seta1.2k

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