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Recent Replies
Answer: Problem using SRAtoolkit
by
GenoMax
125k
Message tells you what you need to do. You need to provide an SRA accession number of name of a downloaded `.sra` file with this command.
…
Comment: mrbayes checkpoint file not starting from linux or windows after accidental clos
by
GenoMax
125k
Information about this issue is posted in a different thead: https://www.biostars.org/p/9552006/#9552599
> Hello Mensur, Could you look a…
Comment: how to do a reliable single cell sequencing analysis?
by
apple4lee
•
0
Thank you for your reply. i followed Seurat tutorial of doing analysis, but I found I use different parameters from that paper. This makes …
Comment: transcriptomincs
by
GenoMax
125k
You can assemble transcripts without using a reference (de novo): https://github.com/trinityrnaseq/trinityrnaseq/wiki
You could then compa…
Comment: How to Calulate Allele Frequency from a VCF File?
by
Emoji
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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…
Comment: 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…
Comment: 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…
Comment: a problem with getBM
by
sanaz
•
0
head(ensembl_ids)
X baseMean log2FoldChange lfcSE stat pvalue padj
1 ENSG00000000938.13 …
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…
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