bambu
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GoekeLab
Reference-guided transcript discovery and quantification for long read RNA-Seq data
Hello, I was wondering how Bambu handles these three alignment cases: 1. Secondary and Supplementary alignments in a bam file? Does Bambu do anything with those or just ignores them?...
Hi there, So I'm trying to look at novel/unannotated isoforms detected and quantified by Bambu and I'd just like some clarification and/or advice. So basically I get an extended annotation...
My bam file was mapped with `minimap2` using the `-ax splice` option against the reference genome of C. elegans. When trying to quantify the data I get the following error:...
In this pull request: - more unit tests are added to check for different cases of alternative splicing in the `compareTranscripts` function. - a more complete documentation of the `compareTranscripts`...
1) In this pull request, I added some unit tests for the writeBambuOutput() function. It tests whether: - the prefix is as expected - the output files go to the...
The unit test & documentation for the `compareTranscripts()` function is incomplete. The test should cover all possible scenarios when comparing two transcripts from alternative splicing events. The documentation should explain...
We've found another odd result in our transcript count data surrounding the gene Apex1 (and at least one other similar gene). This gene has three transcript isoforms that were counted...
DO NOT MERGE - This PR is just for review purposes to make it easier to isolate the NDR changes in the BambuManuScriptRevision branch. This pull request involves several features...
Remove rcfiles input parameter, Now users can use reads with either a vector of .bam paths, a vector of .rds paths, or a list of rcfiles (must be RangedSummarizedExperiment, such...