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Answer: Bam files not accepted in dba.count
by
andreabarghetti
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The same error appears when a sampleSheet with only one line is used.
Reproducible from the vignette data:
library(DiffBind)
…
Answer: Mutation hunting in 100 exome samples
by
soniabedi.07
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Thanks @GenoMax.
So how do I look for common mutations/genes within 100 vcf files?? Do I combine all vcf into 1 or hunt one by one??
Comment: Combine full-length and 3` RNAseq, is it possible?
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benformatics
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To clarify, *it can be done* you could attempt batch effect correction assuming you have comparable time points/experimental replicates. Wo…
Answer: 10x genomics single cell RNA-Seq data submission to GEO
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benformatics
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You could submit the raw data (i.e. 2-4 fastqs) if you wanted and from some perspectives, for instance raw "reproducibility", that might be…
Comment: What does it mean of de.genes in SingleR output? What is the difference between
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Aaron's always got a reason for doing what he does. In this case, it's to show only the reference markers that are *also* differentially ex…
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Going the PLINK / HaploView route would be among the primary ways to do this:
- https://www.biostars.org/p/410870/#411221
- https://w…
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matt
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After all, I realised I don't have that much space on my hard drive, after unpacking these 47 files it would need about at least 750GB.
Ho…
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Hi, please show the output of:
sessionInfo()
str(data1)
Thanks.
Comment: EBI API GWAS query over gene
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sim.j.baum
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Hi Mihai,
I had a look at the output. It works but ... the output is something related to eQTLs. That is close, but its not the (disease) …
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`bcftools` should be your go to choice. Take a look [at this page for querying][1] and [this one for filtering][2].
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Comment: how to identify haplotypes and its frequency based SNP genotyping data?
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curious
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like a haplotype defined by multiple snps? I would imagine you have to code that up in R yourself.
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Check out this recent publication, they used both bulk and scRNA-seq (I am not sure if it is from same individuals). If you read in details…
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Morgan S.
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Yes, this is what I did.
Thanks so much for your quick reply!!
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