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Comment: Is it possible to pass command line arguments to python script in snakemake?
by
Jeremy Leipzig
20k
all this is unnecessary:
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--config', type=str, required…
Comment: Aligning short NGS reads to multiple (100,000) references
by
GenoMax
111k
> 100,000 different sequences be considered low nucleotide diversity?
You had said that each sequence differs by 100 bp that indicates tha…
Comment: Is it possible to pass command line arguments to python script in snakemake?
by
blackadder
•
0
So, you suggest instead of --config use the --configfile and specify the different params in this one?
Comment: Aligning short NGS reads to multiple (100,000) references
by
x_ma_x
•
0
Why would a library of 100,000 different sequences be considered low nucleotide diversity? Those sequences will all be completely different…
Comment: Is it possible to pass command line arguments to python script in snakemake?
by
blackadder
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0
By using the run directive, you cannot use conda environments... I need to load my programs from conda
Comment: single cell RNA-seq: Is there a way to tell if one dataset is more similar to an
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Jautis
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350
No, there's no simple score. That's simply because similarity can be defined so many different ways (distance from the centroid, nearest ce…
Comment: single cell RNA-seq: Is there a way to tell if one dataset is more similar to an
by
454Casull
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Hi Jautis, Thanks for the reply. I guess by saying "similar" is like you have a score-like thing, i.e. the KO score is higher in CT1 than C…
Comment: Betacoronavirus.00.nsq error
by
Sam
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I figured it out, i think. In the handbook I believe they were explaining how they obtained the files when downloaded. When i downloaded an…
Comment: Merge two vcf's, keep only intersection of REF/ALT alleles
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Hello, how would someone do this? From what I can tell, isec produces a list of sites but doesn't produce a merged file. Would you need to …
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Did you manage to download and decompress all the files from NCBI? The command above needs database index files to be there.
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by
Maryam
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Thanks a lot, conlindaven
The genome reference available to me for elemental data is 19 hg.
Do you think I should use **hg 19** or **grch…
Comment: single cell RNA-seq: Is there a way to tell if one dataset is more similar to an
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Jautis
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"more similar" is vague and can be defined different ways. One idea to start with may be to make a UMAP or tSNE plot and see whether your K…
Comment: Betacoronavirus.00.nsq error
by
Sam
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0
now I am getting this ![error][1]
[1]: /media/images/4acf2c37-f00f-4528-aa19-54057b08
Comment: Betacoronavirus.00.nsq error
by
GenoMax
111k
Are you working behind a firewall? Perhaps that is causing the corruption during downloads?
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