User: jean.elbers

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jean.elbers1.6k
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Posts by jean.elbers

<prev • 225 results • page 1 of 23 • next >
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Comment: C: Less and less genes predicted with each iteration of SNAP/MAKER
... I am not sure about comparing `BRAKER2` with just proteins to train Augustus, but in my experience with a Dipteran fly, `BRAKER2` to train Augustus with arthropoda ortho db 10 proteins and species-specific RNA-Seq reads, `BRAKER2-trained Augustus` was comparable to using the `BRAKER2` output process ...
written 8 hours ago by jean.elbers1.6k
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Comment: C: why should we cluster cells when we can label them using databases, in single ce
... My two cents: I think differentiating unknown, novel, and/or deviating from "normal" (whatever that is) cells, seem to be important. ...
written 17 days ago by jean.elbers1.6k
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Comment: C: Imputing missing genotypes using Beagle
... Please see http://faculty.washington.edu/browning/beagle/beagle_5.1_08Nov19.pdf especially section 5 about output ...
written 17 days ago by jean.elbers1.6k
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Comment: C: Imputing missing genotypes using Beagle
... See https://www.biostars.org/p/420990/, I guess that is what you want? ...
written 18 days ago by jean.elbers1.6k
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Comment: C: lncRNA quantification using featureCounts
... You are welcome, no problem. ...
written 18 days ago by jean.elbers1.6k
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Comment: C: lncRNA quantification using featureCounts
... I would not say "without much worrying" as with any experiment, there can be problems in the wet lab that can have some strange influences on the data. I was merely offering a suggestion. The number of counts per sample seems similar based on the data that you have shown. You can search the forum fo ...
written 18 days ago by jean.elbers1.6k
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Comment: C: Imputing missing genotypes using Beagle
... change `-Xmx4g` to `-Xmx100g` or however much ram you have available (use `free -h`) ...
written 18 days ago by jean.elbers1.6k
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Comment: C: lncRNA quantification using featureCounts
... If this is then total RNA-Seq, then the rest (~98%) is perhaps ribosomal RNAs and coding RNAs. ...
written 18 days ago by jean.elbers1.6k
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Comment: C: lncRNA quantification using featureCounts
... Are your input data alignments with mRNA-Seq (poly-A selection) against a genome or transcriptome, and is `annot.gtf` just lncRNAs? Also, how was `annot.gtf` obtained? Edit: do you only have two samples (one biological replicate per treatment)? ...
written 18 days ago by jean.elbers1.6k
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Comment: C: Imputing missing genotypes using Beagle
... Are you trying to impute 3 samples without a reference panel? I do not think this will work well at all. I would think more like 100-1000 **might** be okay. The more the better without a reference panel. ...
written 18 days ago by jean.elbers1.6k

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