User: seta

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seta1.1k
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Posts by seta

<prev • 665 results • page 1 of 67 • next >
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Comment: C: bcftools doesn't normalize the vcf file
... Oh, I knew it for normalizing indels. Is it true for splitting the multiallelic snps? ...
written 4 days ago by seta1.1k
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bcftools doesn't normalize the vcf file
... 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 ...
vcf bcftool normalize written 4 days ago by seta1.1k • updated 4 days ago by harold.smith.tarheel4.2k
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Comment: C: RNA-Seq time series analysis using a DESeq2 spline approach yields far too many
... 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 seta1.1k
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Comment: C: ENSEMBL Gene IDs for Human Inflammation
... Sorry, BioMart from ensembl, where is phenotype section? ...
written 12 days ago by seta1.1k
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Comment: C: Fst calculation between my own population and 1000 genome populations
... 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 seta1.1k
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Fst calculation between my own population and 1000 genome populations
... 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 ...
population 1000 genome fst written 26 days ago by seta1.1k • updated 22 days ago by cetin.m10
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How to compare haplotype with a list of nucleotide variations
... 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 ...
ngs haplotype blood group prediction written 28 days ago by seta1.1k
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Please help with Eagle
... 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= ...
eagle vcf phasing written 5 weeks ago by seta1.1k • updated 5 weeks ago by zx87546.2k
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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 seta1.1k
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Comment: C: Why removing SNPs with MAF<5% for Fst calculation?
... 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 seta1.1k

Latest awards to seta

Popular Question 21 days ago, created a question with more than 1,000 views. For ID conversion by BioMart
Popular Question 28 days ago, created a question with more than 1,000 views. For ID conversion by BioMart
Popular Question 5 weeks ago, created a question with more than 1,000 views. For ID conversion by BioMart
Great Question 8 weeks ago, created a question with more than 5,000 views. For How to remove poly T in RNA-sequencing data
Voter 4 months ago, voted more than 100 times.
Popular Question 4 months ago, created a question with more than 1,000 views. For Differentially expressed gene clustering
Popular Question 4 months ago, created a question with more than 1,000 views. For Differentially expressed gene clustering
Popular Question 5 months ago, created a question with more than 1,000 views. For Differentially expressed gene clustering

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