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Recent Replies
Answer: How to compare the quality of assemblies
by
shelkmike
★
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Since BUSCO results are almost identical but the assembly sizes differ significantly, I suppose that the difference between the assemblies …
Comment: differential gene expression analysis when not all samples have an untreated cou
by
nhaus
▴
300
Thank you very much for your answer, that was very helpful!
> Impossible to say. It depends on your data, particularly on how the donors …
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
by
bk11
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2.3k
This could be because they are probably merging two or more datasets. If you are merging two or more datasets, it will be very important th…
Answer: Problem with Mirdeep2 and Randfold output
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otieno43
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I sorted this out by first removing white space in the first line of the reference genome. Then indexed, the ran the mapper.pl script follo…
Comment: Questions about a bug when transferring cram file to bam file
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Just to be certain, you are saying that if OP runs `samtools view` without the explicit reference it will be automatically downloaded from …
Comment: Questions about a bug when transferring cram file to bam file
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jkbonfield
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That SQ M5 is chr1 in my copy of GRCh38 (Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa).
I'm assuming your hg38.fa is not the sa…
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Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: What happened to Tombo Re-squiggle
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Hi,
Does anybody has the answer to this? I also want to resquiggle my data with Remora but do not quite get which is the appropriate com…
Comment: How To Identify The 16S Rrna Gene Sequence In A Genome
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It's also worth mentioning `Barrnap` is in the bacterial annotation system **Prokka**.
`Prokka` can be installed on Debian systems with `…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
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See also https://www.uniprot.org/help/negative_datasets
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valentinatsar
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Thank you for your response
As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
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me
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750
Ok I made this into an answer. Could you please accept it as such.
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
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me
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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 to compare the quality of assemblies
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GenoMax
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Are there any short read datasets available in SRA? Can you try and see how many left over reads remain after you align to both of your ass…
Comment: Korean human genome reference file
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From NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_001712695.1/
Use the `Download` button or `curl/datasets`.
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