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Answer: Methods for directional pathway analysis of DEGs?
by
Gordon Smyth
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7.9k
limma provides a suite of directional pathway analysis functions that are integrated with its DE procedures. They are based on competitive …
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GenoMax
150k
> It showed me the same positions as that of PrimerBLAST.
So we know that result is correct.
You made the BED file manually? It is in cor…
Comment: MultiQC_report
by
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★
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Thanks for spotting! As mentioned below, it's samples * top adapters. I've made an issue here: https://github.com/MultiQC/MultiQC/issues/31…
Comment: MultiQC_report
by
Phil Ewels
★
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This is exactly the case. Surprising that no-one else has brought this up in 10 years!
I've created an issue here to fix it: https://gith…
Comment: Poor alignment rates using Bowtie
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Quick representative check with a random Illumina dataset (50 bp, 200K reads from it).
Bowtie v.1.3.1 and `mature.fa` downloaded from miR…
Comment: Why does Radian run so much slower than vanilla R?
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I would recommend asking this on the radian GitHub discussion page.
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That being said, I'd like to hear whether the Us in the reference made any difference. It is conceivable that Bowtie 1 treats U as a T.
L…
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> BD Rhapsody protocols
That is important to know. Perhaps the issue is with the way you converted the GFF3 to GTF. What software did you …
Comment: C.reinhardtii single-cell Seurat object - gene names instead of loci
by
Ana
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Thank you for your answer!
Unfortunalety, NCBI doesn't have the latest version of the genome and annotations for this organism (v6.1), so I…
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It is always safer to get sequence/annotations from standard sources like NCBI/Ensembl so no manipulations are required to make the data wo…
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Looking at the size distribution the data must already be pre-trimmed so it does not make sense to trim again. You should merge data from t…
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I think it just counts the total number of lines while there could be multiple adapters types per sample (ex : illumina_universal_adapter, …
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If your reference has invalid bases then you can get quite unexpected behaviors.
I am not sure what takes place - probably the scoring is…
Comment: Is there a tool to obtain GO terms for thousands of genes at once?
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I got it figured out, thanks!
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