saving bambu output to file

[baibhav-bioinfo]

hello,
I have following command to run novel transcript discovery.

se.multiSample_discovery_only_NDR_null <- bambu(reads = c("a6_r1.bam", "a6_r2.bam", "a6_r3.bam", "b6_r1.bam", "b6_r2.bam", "b6_r3.bam", "c6_r1.bam", "c6_r2.bam", "c6_r3.bam"), annotations = annotations, genome = "SbicolorRTx430_552_v2.0.fa", quant = FALSE, NDR = NULL)

now i am trying to save the output in file as, its showing error as shown below

writeBambuOutput(se.multiSample_discovery_only_NDR_null,, path = "./bambu/")
Error in MatrixGenerics:::.load_next_suggested_package_to_search(x) :
Failed to find a rowRanges() method for CompressedGRangesList objects.

kindly help me understand the error and help me save the file

(2) writeToGTF(se.multiSample_discovery_only_NDR_null, "./output.gtf")
this command is working which gives the gtf information of the novel discovered transcripts. Is this information enough to proceed?

[cying111]

Hi @baibhav-bioinfo ,

Thanks for the update.

Just to clarify, writeBambuOutput works with the se output generated from bambu when quant = TRUE, for your reference.

If you are running bambu with quant = FALSE, the se output is a CompressedGrangesList object. You can write it out using writeToGTF to obtain the extended GTF file.

Hope this helps!

Thanks and regards,
Ying

[baibhav-bioinfo]

ohh...now i understand. Thankyou so much