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I'm looking to use flux-capacitor to reference the Geuvadis dataset against gencodeV18.gtf. I want to keep the methodology methodology exactly the same as as was done in the original mapping, changing only the size of the .bam files (sliced BAM).
So far, I have:
ANNOTATION_FILE gencode.v12.annotation.gtf
READ_DESCRIPTOR {ID}/{MATE}[1,2]
ANNOTATION_MAPPING PAIRED
Please could someone let me know the next steps?
Do I need to convert to BED format as stated in Geuvadis Quantifications ?
And what are the exact command line arguments for the annotation using flux-capacitor (identical to the original methodology)?
Thank you in advance,
Chris O