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The annotation standard for proteomics experiments are not clear enough for curators.
Problems that are causing issues:
1. Differentiating between a purification and an enrichment
2. What to …
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Iteratively run cd-hit
sh: line 1: 58934 Trace/BPT trap: 5 /usr/local/bin/cd-hit -i _combined_files -o _clustered -T 1 -M 1800 -g 1 -s 1 -d 256 -c 1 > /dev/null 2>&1
Cant open file: _clustered.c…
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We still have dupliciate entries in the GO database, which makes analyses difficult
These 15 identifiers were found to be ambiguous: ATP6AP2 CALM1 EIF3F GABARAP HIST1H2AI HOXD4 IDS KLK9 MED17 MUC…
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Our ER
UDP-N-acetylglucosamine transmembrane transporter
is picking up this mapping:
https://www.pombase.org/gene/SPBC1734.09
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http://pombase-dev.bioinformatics.nz/gene/SPAC6B12.03c
@Antonialock ?
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- Create method to detect gene function
- Create method to get paralogs for a gene
- Create method to get orthologs for a gene with equal function
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I don't know if manual annotations for "intracellular" are useful or not (we don't use this term).
But we should not get annotations to this term from any inference pipeline.
It's just clutter...…
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This software seems very useful--up to a point. One needs sequence alignments without paralogs to make trees. How can those be filtered out?
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This is more a conceptual question regarding roary than an issue with the software, so please excuse me if this is not appropriate here:
How exactly does the paralog splitting work in roary? In the p…
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Hi Rob,
I'm testing Salmon 0.6.0 in read-based mode and it seems awesome, fast and accurate. Moreover, it's very well documented, which I really appreciate.
My question is about the library type spe…