Closed alexander-schl closed 1 year ago
Hi,
If you print(se)
could you share the output. From these messages it looks like Bambu was successful and the console output is only a series of warnings (that will be fixed in an upcoming version) that do not negatively impact the output.
Kind Regards, Andre Sim
Thank you for your quick response! The output of print(se)
is
class: RangedSummarizedExperiment
dim: 105 1
metadata(2): incompatibleCounts warnings
assays(4): counts CPM fullLengthCounts uniqueCounts
rownames(105): ENST00000190165 ENST00000305248 ... ENST00000622412 ENST00000628764
rowData names(11): TXNAME GENEID ... txid eqClassById
colnames(1): SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000
colData names(1): name
Thanks, yes it looks like your Bambu is installed correctly and you can continue using it without issue. Be sure to patch Bambu once our next version comes out to remove these deprecated warnings.
Hi there,
I use R 4.3.1 and bambu 3.2.6. When using the test set to check if bambu was installed correctly, I encounter the following issue(s) when I execute
se <- bambu(reads = test.bam, annotations = bambuAnnotations, genome = fa.file)
:Can you help me resolve this issue? Thank you in advance!