User: Macspider

gravatar for Macspider
Macspider930
Reputation:
930
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Trusted
Location:
Vienna - BOKU
Twitter:
macspider_music
Last seen:
17 hours ago
Joined:
5 months, 2 weeks ago
Email:
r*********@gmail.com

Posts by Macspider

<prev • 199 results • page 1 of 20 • next >
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Comment: C: GO Term enrichment with poor number of GO Terms
... It is the next step. But first, I wanted to ask what I asked here to be sure that I didn't have any other chance. ...
written 1 day ago by Macspider930
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Comment: C: GO Term enrichment with poor number of GO Terms
... The numbers I provided are already after that stage :( ...
written 1 day ago by Macspider930
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Comment: C: GO Term enrichment with poor number of GO Terms
... My problem is not with my data, but with the paucity of GO Terms for non-canonical organisms (actually for everything that is not human, mouse, fly, thaliana). I was wondering if I was missing something. ...
written 1 day ago by Macspider930
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Comment: C: GO Term enrichment with poor number of GO Terms
... This set of genes host potentially disruptive variants and I already have the proof that the expression is not disrupted. The function however may be. I'm trying to see if they're enriched for any particular function, process or component (*i.e.* GO terms). ...
written 1 day ago by Macspider930
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Comment: C: 1000g database with wrong variant annotation?
... I strongly suggest you to do so and to try to understand every word (it took me weeks). There's a lot of knowledge in there. ...
written 1 day ago by Macspider930
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Comment: C: 1000g database with wrong variant annotation?
... Did you filter the output of `samtools mpileup` without doing `bcftools call` (just a guess)? When you call, only the positions that actually have something to say are kept. ...
written 1 day ago by Macspider930
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Answer: A: genome features and sequence parsing
... You're looking for **getAnnoFasta.pl** from the Augustus programs: http://bioinf.uni-greifswald.de/augustus/binaries/scripts/getAnnoFasta.pl ...
written 1 day ago by Macspider930
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GO Term enrichment with poor number of GO Terms
... Hi all, I have a set of around 250 genes which I'm testing and among everything I am trying I also decided to check if they're enriched for particular GO Terms or gene families. Sadly, I am not working with a well annotated organism, so my GO Term mapping on my genes actually returned only **20%** ...
annotation go terms gene ontology interpro written 1 day ago by Macspider930 • updated 1 day ago by Jean-Karim Heriche9.3k
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Comment: A: 1000g database with wrong variant annotation?
... > is there other way I can validate my pipeline? [...] Maybe there is a reference that is well checked and I can use it for validation of pipeline? My whole life changed after reading this paper: https://www.ncbi.nlm.nih.gov/pubmed/27535533 ...
written 1 day ago by Macspider930
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Answer: A: Fasta to gff with custom set of genes
... > now I cannot simply map all the reads onto this subset and perform DE analysis because I would have normalization bias (using DESeq2 or edgeR), so I need to map all the reads on the whole genome. I don't agree completely. If your reads are RNASeq reads and you map them against a transcriptome, ...
written 4 days ago by Macspider930

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