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Recent Replies
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A: extracting gene names for RNA-seq reads by
florian.bernard5 • 10
As pointed by some of you, there will be cases where it's absolutely impossible to determine if o...
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C: Filtering a vcf file with vcftools, where is my output? by
Shicheng Guo • 6.1k
so what happened if we don't add --recode? if just delete the SNPs from the raw input?
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C: Chromosome lost after merge with vcf-merge by
boymin2020 • 10
Thanks for your advice. **bcftools merge** works much faster and very well.
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C: how can i remove duplicated variants from vcf file? by
Shicheng Guo • 6.1k
Terribile, still have duplicates: [bcftools norm][1] Warning: Nonmissing nonmale Y chromosome ge...
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C: How to get PCA3 and PCA4 from Deseq2? by
cpad0112 • 8.3k
you are correct @ https://www.biostars.org/u/6093/. It stores only pc1 and 2 (https://rdrr.io/bio...
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C: VCF to Bed file format using GATK by
Sa • 0
Thank you so much for your help! I was actually incurring a different error with the GATK comman...
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C: Very low unique mapped reads - STAR alignment by
WouterDeCoster ♦ 31k
Could you naively try to blast a few unmapped reads?
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C: How to get PCA3 and PCA4 from Deseq2? by
h.mon ♦ 18k
`plotPCA( ..., returnData=TRUE)` returns just the first two PCs, hence the need to use `prcomp` -...
-
C: What is the most efficient way to parse a single fasta file which contains over by
Alex Reynolds ♦ 25k
Threads won't help. This is an IO-limited procedure. Computational power is not needed for readin...
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A: How to get PCA3 and PCA4 from Deseq2? by
cpad0112 • 8.3k
May be you can store plotPCA output (with option returnData=TRUE) in an object and plot PCs indep...
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A: VCF to Bed file format using GATK by
chrchang523 ♦ 3.7k
Is there any reason you need to use GATK for this? Just use "plink --vcf [filename] --make-bed".
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A: how can i remove duplicated variants from vcf file? by
Shicheng Guo • 6.1k
Take 1000 Genome phase 3 data as the example: bcftools norm -d both --threads=32 ALL.chr1.ph...
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