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Recent Replies
Comment: Trim CDS to ORF
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jaredbernard
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I tried ChatGPT, but it gave strange answers. See the attempt below. I think it was over-trimming or something, which left me with tiny seq…
Comment: Trim CDS to ORF
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jaredbernard
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I needed to extract them from the transcripts. The genome was annotated by other researchers and I need to use them in my study. I was able…
Comment: Trim CDS to ORF
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jaredbernard
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Yes, the first codon after the offset is methionine. The above solution worked, breaking the process into two phases.
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firestar
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Is it? Is the trajectory purely created from the dimensionality reduction? I assumed the RNA expression matrix was used somewhere? I mean o…
Comment: Z-score for scRNA-seq data?
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I don't think that's correct. For a given gene, z-score of scRNA-seq data could be expression in one cell scaled by mean expression and sta…
Answer: Heatmap of rnaseq data with z-score scale
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There isn't really a problem. Your data is what it is, but I think adding data from a totally different data set is a bad idea. RNASeq is…
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S
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Thank you for your input! And yes I agree with you in terms of the difference in processing, though the workflow was pretty standard except…
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The z-score is the raw score minus the mean of all samples, divided by the standard deviation so if you add samples, then you change the z-…
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![Figure1][1]
![Figure2][2]
[1]: /media/images/ccd91222-df0a-4c33-984f-61fb94dc
[2]: /media/images/50856040-0bf9-4389-85da-7ae…
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Thanks to everyone, I appreciate the support :)
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OK, thanks.
Did maker (or Braker, or ... the annotation tool you used) not provide the corresponding CDS file of the annotations then? Do …
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goh, if there are not too many of those it could be fine indeed.
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Aha, I suspected something like this already :) :
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Nanopore sequencing is worth trying. You should be able to see the deletion.
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