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

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  1. Thasso Griebel

    Hi Chris,

    we used .bed files for Geuvadis basically because .bam support was not ready yet. You can go and convert to .bed and then use the same parameters as we used for Geuvadis (the parameter file is listed here. On the other hand, you can also go ahead and do the quantification with the .bam files. For that, just go with the default parameters like this:

    #> flux-capacitor -i <bam> -a <gtf> -m PAIRED -o result.gtf