Reference file in MapDamge2

[jimmybee]

I am new to bioinformatics, so please forgive me for this simple question!
I am trying to use MapDamage2, and am not sure how to format the reference file. It is currently in .fasta, and was ok the bowtie/samtools pipeline I used, but I don't know how to change it so it works with MapDamage.... any suggestions would be much appreciated.

$ mapDamage -i /Users/name/IonXpress_..._55.sff.raw.bam -r ref.fasta
Error: 'ref.fasta' is not a valid file
Option parsing failed, terminating the program

Maybe try the full path of the file (like what you did for the input file).

[Cat_J]

I am new to bioinformatics, so please forgive me for this simple question!
I am trying to use MapDamage2, and am not sure how to format the reference file. It is currently in .fasta, and was ok the bowtie/samtools pipeline I used, but I don't know how to change it so it works with MapDamage.... any suggestions would be much appreciated.

$ mapDamage -i /Users/name/IonXpress_..._55.sff.raw.bam -r ref.fasta
Error: 'ref.fasta' is not a valid file
Option parsing failed, terminating the program