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  • jimmybee
    replied
    Originally posted by Cat_J View Post
    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).

    Leave a comment:


  • Cat_J
    started a topic Reference file in MapDamge2

    Reference file in MapDamge2

    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

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