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Comment: About calculating the GC content in a sliding window
by
schlogl
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110
Hi GenoMax, hope everything is ok with you bro.
Do you know if I can use bedtools makewindow approach to multifasta fileas? I take a look a…
Answer: error while testing nextflow with --genome GRCh38
by
Matthias Zepper
▴
970
I suppose because you are actually providing two reference genomes here at the same time? When you specify the `test` profile, it loads a s…
Comment: error while testing nextflow with --genome GRCh38
by
Pierre Lindenbaum
146k
there must be a hidden file `.nextflow.log` in your working directory. Show use the lines in the context of the error (java stack trace).
Comment: error while testing nextflow with --genome GRCh38
by
Barry Digby
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980
Dedicated resources for nextflow queries:
[https://nf-co.re/join/slack][1] **help** and **rnaseq** channels in your case.
&
[https://git…
Comment: Combine metadata
by
Ram
36k
Have you tried adding debugging statements to check if each line is reached? What have you tried on your own?
Comment: select rows in a tab-delimited ed file
by
cpad0112
21k
$ awk -v OFS="\t" -F "[:|]" '{print > $6".txt"}' test.txt
Comment: Metabolomics log-transform or standardize for WGCNA
by
obidobi
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30
Thaaaanks a bunch!
Btw, since **log2** transformation could generate some negative values (some of my concentrations are quite low), I wa…
Comment: Script or tool to compare more than two .cls files in R or Python
by
Alex S
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0
They have the same cluster name but no correspondence for those names.
**As such, you need to identify which lines are in common and then …
Comment: Is it possible to pass command line arguments to python script in snakemake?
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Ecstasia
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0
I wouldn't agree that you never need to pass arguments to a python script in a snakemake workflow.
What if the python script you're trying…
Comment: Logfold change
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rpolicastro
8.9k
If any of the means are 0 you should add a pseudocount to all values too.
Comment: gsea msigdb RNA-seq input file
by
rpolicastro
8.9k
What guide are you referring to specifically? There are a few popular implementations of GSEA.
Answer: Logfold change
by
jared.andrews07
★
13k
`log2(mean(group1 samples)) - log2(mean(group2 samples))`
Repeat as needed for whatever comparisons.
Comment: Metabolomics log-transform or standardize for WGCNA
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Kevin Blighe
82k
Hi Nilay, we followed the 4-step filter procedure above (I just modified my post), and then always logged (natural log) followed by Z-trans…
Comment: Which strand specific option need to be used with HISAT2?
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Antonio R. Franco
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4.8k
It is very convenient to use the pseudo mapper [salmon][1] with the `-l A` option. Salmon evaluates all forms of strandness at the same tim…
Comment: Metabolomics log-transform or standardize for WGCNA
by
obidobi
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30
Hi Kevin,
Thanks for an excellent summary!
I have a Q related to this topic, do you think both normalizing and log transformation are re…
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