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:
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,