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Answer: What is the NCBI's definition of an "atypical genome"?
Comment: GO enrichment analysis
Comment: GO enrichment analysis
Answer: What is the NCBI's definition of an "atypical genome"?
A: Why is RNA-Seq or cDNA used to detect gene fusions instead of gDNA?
Answer: Somatic truth set
Comment: Best way to visualize .paf or .sam alignment to a fasta file
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Recent Replies
Answer: PTM-aware protein folding / docking
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Mensur Dlakic
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Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1]. Not to discourage…
Answer: Admixture cv error
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Declan
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I had this issue today and was able to resolve it by changing the random seed Admixture uses by adding `-s time` (which sets the random see…
Answer: Total No of Genes of GENCODE Release 43
by
ahmad
• 0
The following is the correct code gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf') dtgtf_43<-data.frame(gtf_4…
Comment: Total No of Genes of GENCODE Release 43
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ahmad
• 0
Hello, thanks for replying, by mistake I paste the wrong code. the following is the corrected gtf_43<-rtracklayer::import('gencode.v43…
Comment: Kallisto bustools for scRNA-seq
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dsull
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I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
Comment: Aberrant splicing in bulk RNAseq
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dsull
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First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
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There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6. There is also a CNA preprint from years ago b…
Comment: Somatic truth set
by
lethalfang
▴ 90
Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/ho…
Comment: How to get subset of a Seurat object based on metadata?
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jv
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Hmm, not sure why `subset` doesn't match to '0:CD8 T cell' but maybe it's the ":"? An alternative option is the following: ``` idx <- whi…
Comment: GO enrichment analysis
by
Jeremy
▴ 780
g:Profiler has an Arabidopsis option: [g:Profiler][1] [1]: https://biit.cs.ut.ee/gprofiler/gost
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The first job is a nightmare and you will need some luck. I understand you're looking for an industry offering. Unfortunately I've worked o…
Comment: Best way to visualize .paf or .sam alignment to a fasta file
by
GenoMax
127k
Why not use IGV with SAM file? If you want a text based viewer then ASCIIGenome: https://asciigenome.readthedocs.io/en/latest/
Answer: What is the NCBI's definition of an "atypical genome"?
by
MirianT_NCBI
▴ 510
Hi, You can find more information about what constitute an [atypical genome in this FAQ][1]. Here's the list of reasons for a genome to …
Comment: How to get subset of a Seurat object based on metadata?
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sunyeping
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> skin$predicted_cell_type Error in rep.int(x = colnames(x = x), times = length(x = i)) : unimplemented type 'NULL' in 'rep3…
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chi.delta
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Let's say that based on known FACS data, I already know that three populations exist based on the two antibodies staining: single positive …
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