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Apart from miRNAs matching the miRBase sequences, we also counted reads mapping to each type of isomiR.
All probesets mapping to each gene were retrieved based on information at NetAffx.
We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture.
For example, the eve cutoff was computed as the highest observed score outside of a coding region for the Drosophila eve locus mapping to each of the tephritid gt, Doc1 and pnr loci.
We then compared the number of reads mapping to each of the genes in both species.
This module counts the number of bases mapping to each exon and splice junctions.
HTSeq was used for quantifying the number of reads mapping to each gene.
The number of reads mapping to each accession for each sample is shown in Table 1.
We then counted the number of reads mapping to each exon unit.
A cluster is defined as ≥3 contiguous genes (with ≥50 small RNAs mapping to each gene).
From the female pool, the number of reads mapping to each block is similarly constant, at roughly 150.
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