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Comment: interpretartion of a vcf file
by
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In my case , there is only one sample :
here is an example of a some variants generated using minipileup :
#CHROM POS ID REF ALT QUAL FI…
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This should work if you know your sequences are related and can be globally aligned; otherwise it is safer to compute local alignments (for…
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A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
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What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
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After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1])
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atowns21
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Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome.
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The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
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There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
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Hmm, okay I'm not sure what is going on, but here is what I did:
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Ok, thank you so much~
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I have 2 files output, no error logs...
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agree.
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This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
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