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Recent Replies
Comment: How to Calulate Allele Frequency from a VCF File?
by
Emoji
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0
Thanks, but how do i do that?
Answer: transcriptomincs
by
Apex92
▴
240
Yes, you can use a reference genome from a related species to assemble transcripts of a target species. This approach is known as ```de nov…
Answer: How to continue a interrupted MrBayes tree analysis?
by
omaridris5315
•
0
Hello Mensur,
Could you look at my case too? interruption issue but a different error. This is the second time I face and I rerun it. I ha…
Answer: mrbayes checkpoint file not starting from linux or windows after accidental clos
by
omaridris5315
•
0
my convergence value at 23 million run for last 10 days was at .017623 something. out of 7 million more remaining.
Comment: How to calculate Minion run time needed?
by
andres.firrincieli
3.1k
> Does someone know how to calculate how many hours (approximately) i
> need to run an minion, to get a good coverage for example of bacter…
Answer: how to do a reliable single cell sequencing analysis?
by
ATpoint
68k
The usual approach for starters would be to follow guided and well-accepted tutorials.
That would (incomplete list) be:
- The Biocon…
Answer: a problem with getBM
by
sanaz
•
0
head(ensembl_ids)
X baseMean log2FoldChange lfcSE stat pvalue padj
1 ENSG00000000938.13 1344.2587 2.107…
Answer: Recommendations needed for a tool for comparative gene set enrichment analyses v
by
fuellen
▴
20
Hello and Thanks!
OK, I should have written "The gene lists I have prepared" instead of "The DEG lists I have prepared".
In any case, is …
Comment: a problem with getBM
by
Mike Smith
★
1.9k
Can you update your post to show some examples of what's in your `ensembl_ids` object? Perhaps the contents of `head(ensembl_ids)`.
It's …
Answer: trainGlimmerHMM Error while training a genome
by
congliu37
•
0
Hello,
I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File?
by
Jeremy Leipzig
21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)?
by
Fabio Marroni
★
2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism
by
Rob
▴
160
Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers
by
Pierre Lindenbaum
152k
> with nucleotide numbers and DNA/prot aligned line by line
what does it mean ? Create a Minimal, Reproducible Example to enable others t…
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