Hi all,

Hopefully this is the correct place to ask this question.

I'm looking to use flux-capacitor to reference the Geuvadis dataset against gencodeV18.gtf. I want to keep the methodology exactly the same as was done in the original mapping, changing only the size of the .bam files (sliced BAM).

So far, I have:

  • Downloaded all .bam files for CEU population from ArrayExpress
  • Sliced bam files for particular genomic locations using samtools.
  • Sorted and indexed bam files.
  • Downloaded gencodev18.gtf  
  • Created parameter file:
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