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A: Create bigwigs in python?
Create bigwigs in python?
Create bigwigs in python?
Answer: Logfold change
Comment: Logfold change
C: Do you know some scripts to plot MAKER annotation results?
Answer: BWA MEM Multiple Primary Alignments
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Recent Replies
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schlogl
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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
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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
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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).
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Dedicated resources for nextflow queries: [https://nf-co.re/join/slack][1] **help** and **rnaseq** channels in your case. & [https://git…
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Have you tried adding debugging statements to check if each line is reached? What have you tried on your own?
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$ awk -v OFS="\t" -F "[:|]" '{print > $6".txt"}' test.txt
Comment: Metabolomics log-transform or standardize for WGCNA
by
obidobi
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Thaaaanks a bunch! Btw, since **log2** transformation could generate some negative values (some of my concentrations are quite low), I wa…
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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 …
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Ecstasia
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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
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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
by
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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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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
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obidobi
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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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