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[question]: Is it possible to run bambu with >2 conditions #491
Description
Hi @cying111 and @andredsim
Is it possible to run bambu with bams from more than 2 conditions - in this case, the different bams were obtained after using minimap2+samtools on the ONT fastqs
sample,replicate,bam,condition
WT,1,path_to_WT_1.bam,control
WT,2,path_to_WT_2.bam,control
CL_1,1,path_to_CL_1_1.bam,CellLine_1
CL_1,2,path_to_CL_1_2.bam,CellLine_1
CL_2,1,path_to_CL_2_1.bam,CellLine_2
CL_2,2,path_to_CL_2_2.bam,CellLine_2
The help text here states this
if you plan to do comparative analysis between conditions, it may be beneficial to run all samples together instead of individually
I tried finding the answer, but could not and this might be similar/close to #393
Thanks in advance.
Activity
cying111 commentedon Jun 13, 2025
Hi @tamuanand ,
Yes, you can run bambu on data with more than two conditions if you plan to compare them. Running the samples together ensures a shared annotation file, making downstream analysis easier without needing to match references across samples.
To run bambu for multiple samples, you can follow the instructions here:
se.multiSample <- bambu(reads = c(test1.bam, test2.bam, test3.bam), annotations = gtf.file, genome = fa.file)Hope this clarifies your question!
Thank you
Ying