Hi,

 

I'm annotating some filtered, sorted bam files with their index files and when I run:

flux-capacitor -p <parameter_file> -i <sample.bam> -o <output.gtf>

with:

ANNOTATION_FILE gencode.v12.annotation.gtf
READ_DESCRIPTOR {ID}/{MATE}[1,2]

ANNOTATION_MAPPING PAIRED

I get "You cannot specify a READ_Descriptor for BAM files".

I see this has been raised and apparently resolved in 

It still seems to occur. I'm using Win 7 OS 64bit - flux-capacitor-1.5.2.

 

Any prompt help will be great!

Thanks. 

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1 Comment

  1. Emilio Palumbo

    Hi Chris,

    as the error message says, you cannot specify a read descriptor for BAM files. In order to run the quantification you should remove the read descriptor line from your parameter file. The parameter file should then look like this:

    ANNOTATION_FILE gencode.v12.annotation.gtf

    ANNOTATION_MAPPING PAIRED

    Hope this helps.

    Best,

    Emilio