FlyBase used samtools to filter for uniquely mapping reads ( NH:i:1 ) from the original FlyAtlas2 bam files; samtools was also used to calculate the number of mapped reads. The bedtools genomecov function was used to generate bedGraph coverage data from bam files. An in house FlyBase script converted bedGraph coverage data to wig format. Read length was obtained from related SRA accessions.
Reads from 2 biological replicates were aligned to Dmel_Release_6 reference genome, Ensembl BDGP6, dated March 2016, as provided by Illumina, using the Tuxedo pipeline. The resulting bam files were merged.