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Recent Replies
Answer: Is a human genome file with reference as NCBI37 the same as hg19?
by
GenoMax
129k
If you go to the GRCh37 page at NCBI you will see that `hg19` is a synonym (mostly used by UCSC as I recall): https://www.ncbi.nlm.nih.gov/…
Comment: Help with running ATAC using Encode pipeline
by
Chris
▴
100
So do we have redundant in this case when we specify the path to fastq.gz files in both input file and json file? json file is .json, how a…
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
▴
110
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
▴
70
Trying to do so ))
Comment: Help with running ATAC using Encode pipeline
by
rfran010
▴
110
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 ?
by
Vincent Laufer
★
2.9k
does this mean you understand pident now and are moving forward?
Answer: Random dataset and DESeq2
by
Vincent Laufer
★
2.9k
@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?
by
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
by
Sib
▴
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…
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