User: predeus
predeus • 1.2k
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Posts by predeus
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... Dir paths look kind of funny. Did you try running the commands mentioned in the debug manually?
Try checking what "Trinity.fasta.bowtie2" actually is - is this a wrapper script? ...
written 8 weeks ago by
predeus • 1.2k
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... You probably would want to map the reads back to the assembly and then evaluate sequence duplication. FastQC works with raw reads and has limited power to inform you about the nature of your problems.
If after paired-end mapping you still get high duplication rate, you probably are dealing with PC ...
written 8 weeks ago by
predeus • 1.2k
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... I'd also like to add that if 80% of variance in your 20-sample RNA-seq PCA is explained by PC1, there's either something very wrong with your samples, or with the way you are analyzing your data. Make sure they are log-transformed and normalized - ideally with something like vst or rlog transformati ...
written 8 weeks ago by
predeus • 1.2k
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Comment:
C: Principal Component Analysis PCA
... They must have only ran it on SNPs :) basically, the number of PCs = number of rows.
Rows could be genes (for RNA-seq), SNPs, or anything else. ...
written 8 weeks ago by
predeus • 1.2k
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... In case somebody is searching this: newest version of InterProScan works very nicely and adds GO terms as well as Reactome pathways to the annotation based on discovered domains. Of course, these approaches have a bunch of limitations, but still - I think this is the easiest way to do it. Took me ab ...
written 8 weeks ago by
predeus • 1.2k
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... Wow, thank you. It takes a little while to get InterProScan running, but once you got it going, it's quite.. impressive. ...
written 8 weeks ago by
predeus • 1.2k
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... Thank you, I'll give it a shot. ...
written 3 months ago by
predeus • 1.2k
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... Hello all,
I was wondering if there is a good tool for annotation of eukaryotic genes obtained by gene prediction, for example, by Braker pipeline (or any other gene prediction pipeline for that matter)? By annotation I mean basically blasting and hmm-scanning putative proteins against various dat ...
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... In case somebody is looking through this: it was a bug and it was fixed. The current version works OK. ...
written 3 months ago by
predeus • 1.2k
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Answer:
A: RepeatMasker on new species
... Does anybody know how crucial it is to use your own repeat library in order to successfully mask repeats? I know it would depend on species, of course. Is there much difference in the amount of sequence masked?
Thank you for any input. ...
written 3 months ago by
predeus • 1.2k
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