I called peaks using MACS2 and now would like to use my narrowPeak file to do featureCounts. As far as I can tell, featureCOunts only uses SAF or GFF formats. Does anyone know an easy way to convert between a bed and these file types for Dm3?
The first column is the identifier. This is then either any gene name or in case of genomic regions simply the concatenated genomic coordinates, e.g. separated by dot, such as chr1.100.1000000. For genomic regions I always set strand to ., for genes one can set the strand where the gene is located.