User: seta
seta • 1.1k
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Posts by seta
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... Oh, I knew it for normalizing indels. Is it true for splitting the multiallelic snps? ...
written 4 days ago by
seta • 1.1k
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... Hi all,
I'm trying to normalize a vcf file using bcftools `(norm -m -any`), but it didn't normalize the vcf file without returning any error. Actually, the vcf file was the same before and after normalization! could you please give me any suggestions about the issue, what's the problem?
Thanks ...
written 4 days ago by
seta • 1.1k
• updated
4 days ago by
harold.smith.tarheel • 4.2k
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... You're working with big data and getting such a result is not odd. I think 15000 DE genes is normal for RNA-seq data analysis ...
written 8 days ago by
seta • 1.1k
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... Sorry, BioMart from ensembl, where is phenotype section? ...
written 12 days ago by
seta • 1.1k
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... I wanted use vcftools for fst calculation, I merged vcf files using bcftools, but couldn't successfully calculate fst on the merged vcf file. Could you please share your script? ...
written 22 days ago by
seta • 1.1k
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... Hi all and Merry Christmas!
I would like to calculate Fst for some selected SNPs between my own population (the variants came from whole-genome sequencing of about 800 individuals) and other populations in 1000 genome. To this end, I extracted the variants of interest using VCFtools with --recode ...
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... Hi all,
I am trying to predict blood group from whole genome sequencing data (human); I found that this [database][1] is helpful. To this end, after variant calling and phasing vcf file, the haplotypes should be extracted and compared with information in the above-mentioned database, yes? Could you ...
written 28 days ago by
seta • 1.1k
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... Hi all,
I got a vcf file of a single chromosome containing about 1121 samples (derived from whole genome sequencing) for phasing by Eagle2, but it returned the below error:
[E: vcf_parse_format] Number of columns at chr9:133255595 does not match the number of samples (1120 vs 1121)
Read M= ...
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Comment:
C: VCF file phasing by SHAPEIT
... Thanks, Kevin for your nice point. At the moment, I would like to try Eagle 2 due to the more accuracy and speed compared to Shapeit as its authors said. ...
written 6 weeks ago by
seta • 1.1k
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... Thanks a lot for your explanation. So, in your opinion, is it better to calculate the Fst for lower frequency and common variants, separately rather than removing some variants?
Agree with you about the common variants and disease, thanks for correcting me.
In this [paper][1], the authors mentio ...
written 6 weeks ago by
seta • 1.1k
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