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Hello,
First of all: thank you very much for sharing this code with very clear description here!
After running the PAQR pipeline successfully, I am getting a list of differential usage of polyA…
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I'm currently struggling with failure on detecting most distal polyadenylation site even though I used `--no_redundant longest` option in `flair collapse`. While examining the code, I've found out two…
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After many single-step process obsoletions this branch is more organized:
mRNA polyadenylation children have now all been rehoused or obsoleted (this will go in the next week or so)
Next ta…
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Need to check this (I.e other annotations), but I'm pretty sure that this is referring to TRAMP-exosome dependent pathway. However the current labels are problematic because MOST other unrelated RNA …
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Need to curate some alternative transcript examples for Chado loading
can do some from the gene expression list:
gene expression, alternative splicing (3)
gene expression, alternative transcri…
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https://www.biorxiv.org/content/early/2018/04/12/300061
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https://en.wikipedia.org/wiki/Cleavage_and_polyadenylation_specificity_factor
CPSF4 | Cleavage and polyadenylation specificity factor subunit 4 | | mRNA export from nucleus | | Reactome | Hom…
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Thank you for your tool.
I'm sorry to bother you,I don't quite understand what the output content means.
Accodition to the acticle, If I want to filter the data I need to set the cutoff of adjusted…
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> What do we have annotated as "residue extensions"
I cheated and looked in the GAF file rather than querying Chado. There are 15 annotations with a `residue()` or `modified_residue(…
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Hi dear,
Could you please explain to me what is the APA columns in the differential expression file and the decision file?
I checked the coordinates reported in those column using ensembl ad they …