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A: Best Practice On Variant Discovery For Bacteria?
Comment: Error with BiocParallel. No barcodes files found
Answer: What is the bin size for Bamcompare?
Answer: What is the bin size for Bamcompare?
Answer: Random Access remote BAM files
Answer: How to interpret this plotMDS of three disease clusters?
Comment: How to interpret this plotMDS of three disease clusters?
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Answer: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool
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Michael
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Variants should be called using a specialized mitochondrial variant caller, e.g.: [GATK Mutect2 CallMt][1] Then, pi, Tajima's D, and oth…
Comment: Splitting query fasta file for Diamond Blastp make the process faster?
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kmat
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I used `seqkit split` to divide the query FASTA file into 10 parts and then ran `diamond blastp` on each file using 44 threads. The process…
Comment: Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLI
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zx8754
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Try: `--covar-name SEX,PARKISON` FID and IID are Family ID and Individual ID, they are not covariates. Side note, if PARKISON means "Par…
Comment: Error with BiocParallel. No barcodes files found
by
bio_info
▴ 10
I understand, thanks for explaining this to me. I'll take care of this in future.
Comment: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool
by
Pierre Lindenbaum
162k
> , but I was unsuccessful. what does it mean ?
Answer: Does prokka work the same on forward and reverse complementary reads?
by
igmin
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Prokka works the same on both forward and reverse complementary reads. It doesn't matter if your genetic sequences are in their original fo…
Comment: Construction of circos plot from WGS data
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Anitha
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Thank you for the information. But, I am still struggling like which data to use and how to process the input data to represent to build th…
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cmdcolin
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is there any reason why you do not like tools based on read depths?
Comment: CreateSeuratObject taking very long
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eae6d2e7
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Thank you for your reply! I followed your advice to convert to sparse matrix first but I got this error Error in Matrix::sparseMatrix(raw_…
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ericrkofman
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I can't find an hg38 version, and the old VCF seems to be of a different header format so I am having difficulty converting it to hg38 from…
Comment: What is a good way to do gene differentials in single cell data where one group
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ATpoint
82k
Preferred if you have true biological replicates. Can still be combined with my subsetting strategy, like use 100x different cells for the …
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ATpoint
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```r set.seed(1) m = matrix(rnorm(100), nrow = 10) rownames(m) = 1:10 # normal ha = rowAnnotation(foo = anno_mark(at=1:nrow(m), labels=row…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
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Ram
44k
Please do not add answers unless you're actually answering the question. I've moved your post to a comment.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
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I still cannot find a way. It seems to be an easy to solve issue and I was trying any possible combination with the aforementioned gp=gpar(…
Comment: What is a good way to do gene differentials in single cell data where one group
by
fracarb8
★ 1.6k
I would probably use a pseudobulk approach.
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