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GoekeLab / bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data
GNU General Public License v3.0
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Tracking read-to-transcript assignment #332

Closed sunsetyerin closed 1 year ago

sunsetyerin commented 2 years ago

Hi, @andredsim @cying111

I want to use the feature of Bambu tracking read IDs. From the previous issue, it appears like a different branch is merged into the feature. Wonder if the feature is merged into the main branch.

sunsetyerin commented 2 years ago

I managed to run bambu with trackReads = T

image

Can you please help me with solving the error?

cying111 commented 2 years ago

Hi @sunsetyerin , this is caused by a bug in the quantification step related to multiple assignment across genes, we are working on this now and will get back soon.

sunsetyerin commented 2 years ago

@cying111, okay then please let me know if the update is finished

cying111 commented 2 years ago

Hi @sunsetyerin , the bug is now fixed in the master branch, you may try to re-run your sample. Let us know if the same error perists or there are any other errors! Thank you

sunsetyerin commented 2 years ago

@cying111 thank you so much. Was able to run bambu and got se object with readIDs but is there any ways I can match read IDs with gene IDs?

andredsim commented 2 years ago

Hi,

Since you already ran bambu with TrackReads = TRUE, you can access the read id to genes map using metadata(se)$readToTranscriptMaps. Under the column equal matches, is the index for the gene found in rowRanges(se).