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Recent Replies
Comment: Is a human genome file with reference as NCBI37 the same as hg19?
by
a5864557
•
0
Note: I've also asked this [here][1]
[1]: https://bioinformatics.stackexchange.com/questions/21101/is-a-human-genome-file-with-referenc…
Answer: [Meta] Use of AI
by
GenoMax
129k
As you indicate, AI in some form or other is here to stay and we can't avoid it in our lives and on biostars.
Main issue I see is the vali…
Answer: RNASeq gene labeling and mRNA filter from bulkRNA data.
by
rfran010
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100
featureCounts can extract this information and output a column for you during counting, presuming you input a GTF file.
`extraAttributes …
Comment: What are recommended parameters for the local protein alignment ?
by
Alexander
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70
Trying to do so ))
Comment: Help with running ATAC using Encode pipeline
by
rfran010
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100
The "Input files" section is details on how you can specify your fastqs in the JSON. (You specify all pipeline parameters in the JSON.)
Ess…
Comment: What are recommended parameters for the local protein alignment ?
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Vincent Laufer
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2.9k
does this mean you understand pident now and are moving forward?
Answer: Random dataset and DESeq2
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Vincent Laufer
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@e38da452
Not only is this not surprising, it is the basis for an entire class of statistical techniques referred to as permutation bas…
Comment: (ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now
by
GenoMax
129k
> This generated multiple Trinity.fa files in the index folder
Did the process complete successfully?
Comment: Random dataset and DESeq2
by
LChart
2.6k
I don't think you've given enough detail about your approach (what's the data? are you correcting for covariates? how did you shuffle? how …
Answer: Network cross-validation
by
LChart
2.6k
What do you mean by "robust" in this case? Which of the following is closest to what you want to estimate:
(1) Would I get a similar res…
Comment: I have one fasta file of a bacteria. Can i use to create a phylogenetic tree?
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Mustafa
•
0
Thank you so much ! will try them all !
Answer: I have one fasta file of a bacteria. Can i use to create a phylogenetic tree?
by
andres.firrincieli
3.3k
If the fasta file contains the genome sequence you can use the following:
1. GToTree (see example [here][1])
2. [GTDB-tk][2] *de novo…
Comment: Low mapping percentage
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Sib
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40
Thank you for the reply @genomax .
If there is not much I can do about the contamination at this stage, what is the benefit of knowing the…
Answer: integrate single cell RNA sequencing data
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Hamid Ghaedi
2.9k
There are different approaches that you may choose to deal with batch correction. Harmony is one of those approaches that has been shown to…
Comment: What does canonical transcript mean in the context of VEP
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Vincent Laufer
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@curious - The only thing I have to add to @yokofakun 's precise answer is that, while you are considering and reading about Ensembl canoni…
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