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Code should be placed in three backticks as shown below

Hello sir, 
I am trying to run Bambu for my files. I input .bam.file, gtf.file, and fa.file as per requirements but my files are not processing. I have checked the file format too to find out my mistake. But as far now I couldn't resolve this error. Please help me to run my files. I have attached the image of run commands. 

# please also include the results of running the following in an R session ![ /media/images/dd152eae-c26c-4560-b29e-0dda4ddd][1]

sessionInfo( )

Hi Sheetal,

test.bam, fa.file, and gtf.file should all point to files. You could use test.bam <- "1A.bam", fa.file <- "out.fa" and gtf.file <- "out.gtf". (if these files exist in your working directory). The system.file command looks for the data that comes with the bambu package, that is not needed for your own data (and won't work).

Thanks!

Jonathan