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In the [tutorial documentation](https://funannotate.readthedocs.io/en/latest/tutorials.html#non-fungal-genomes-higher-eukaryotes) for higher eukaryotes there are a few suggestions about additional par…
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I'm trying to run kb-python in 10X v1 data. I've previously runner kb on drop-seq and 10X v2 data. However, with 2 diff…
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Hi Jon,
Unfortunately I decided to stare at my annotations again...and I think I could do better.
I was just wondering if there was a specific reason not to include PASA models beyond the ones t…
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Hi all,
sorry if this is not the correct channel to ask this but I have a question regarding how the PSI is calculated for the cases of intron retention, specifically which isoforms are selected to…
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I've been an ardent user of kb_python since it's release but I've just noticed some striking differences with the lamanno flag generated reference versus the "normal" reference generated from the same…
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Im really enjoying playing around with monocle3 and have a quick, and probably naive question.
Given that pseudoalignment is marked by the roots of the trajectory, which are defined by identifying …
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Hi there,
The new version you published yesterday is something I really need at the moment! My problem is that I tried to generate a genome-position-based bam file and IGV is not displaying anythin…
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I have been continuing to have issues with the set of code to make the test data work. here is the full run result I keep getting:
2020-02-27 14:19:32,198 INFO - Workflow polling stopped
2020-0…
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I am trying to run the R notebook [Analysis of single-cell RNA-seq data: building and annotating an atlas](https://colab.research.google.com/github/pachterlab/kallistobustools/blob/master/notebooks/k…
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Hello guys,
Thanks for your nice welcome in Lausanne. I'm now trying to run BgeeCall in Lyon. It is working fine on a mac, but using my ubuntu is does not work properly. I also tried to launc…