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Answer: Assume "yes" as the answer to any prompts with bioconda
Answer: Assume "yes" as the answer to any prompts with bioconda
Comment: biomaRt error for different R version
Answer: What is the normalization status of metabric data?
Answer: Assume "yes" as the answer to any prompts with bioconda
Answer: Assume "yes" as the answer to any prompts with bioconda
Answer: biomaRt error for different R version
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Answer: DEseq2
by
ATpoint
81k
The DESeq2 input is a numeric count matrix (or data.frame) with rows being genes/observations and columns being samples/cells/specimen. Ple…
Comment: How to add motifs in cellranger-arc reference?
by
Ehsan
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Hi. Do you have any updates on what you ended up doing? I am encountering same issue, cannot really find a good TF motif database for zebra…
Comment: biomaRt error for different R version
by
manaswwm
▴ 490
Wonderful, and thanks for tagging Mike! For those who come back for this problem, the following seemed to work for me: Downgrading `dbply…
Answer: Assume "yes" as the answer to any prompts with bioconda
by
Juke34
8.5k
From my experience using `biocontainers` base container no need to set `yes` installation is done without any command prompt, otherwise as …
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
by
Dave Carlson
★ 1.7k
You're allocating 4 compute nodes (`#SBATCH -N 4`), but STAR can't actually make use of more than 1 compute node. You can increase the num…
Answer: Assume "yes" as the answer to any prompts with bioconda
by
Dave Carlson
★ 1.7k
```conda install -y bioconda::packageX conda-forge::packageY``` should do what you're looking for.
Comment: Supergnova stuck in tutorial
by
Murat
• 0
Hi GenoMax, Thank you for your advice. I sent an email to them and have already opened an issue on Github. Let see if there is any other so…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
You can't. The data does not exist. UniProt only annotates where a lysine is know to be acetylated. There is no way that UniProt can know w…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
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Jacky
• 0
Yes, that's what I meant.
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
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Jacky
• 0
I'm sorry, I didn't explain it clearly. Below are my operational steps: I enter 'Triticum aestivum' in the search box and perform a search.…
Comment: Indexing the Reference Genome is not done in STAR
by
n_navy
• 0
I add these parameters; #SBATCH -N 4 #SBATCH --tasks=1 #SBATCH -c 4 #SBATCH --time=24:00:00 But it keeps giving error
Comment: RNA seq differential expression analysis
by
rrehimi
• 0
Thanks! Could you please explain the DEseq2 method using Galaxy step by step? Input files?
Answer: Korean reference file
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colindaven
6.3k
Is is this one - KOREF ? There might be multiple versions. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA294231/ If it is, then take that…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
The question is not quite clear? are you asking for wheat proteins in UniProtKB which contain a lysine amino-acid, where those lysine are *…
Comment: RNA seq differential expression analysis
by
seta
★ 1.9k
You should provide row count (without normalization) for doing DEG analysis by relevant tools such as, edgeR or DEseq.
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