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Protocol publication

[…] d a putative insertion when the blast hit had the same smallest e-value for more than one TE family. We required a putative TE call to have at least 100 bp, at least 80% identity to canonical TEs, and merged TE calls of the same family and within 500 bp. TEs of different families but were within 2 kb were called as putative TE clusters and excluded from the analysis. In both species, we excluded INE-1 TEs, most which are relicts of a TE family that experienced an ancient burst of transposition events and are now mostly fixed in populations (; ). Our study included 255 TEs for the Oregon-R strain, 419 TEs for RAL strains, and 349 TEs for the D. simulans strain., Raw reads were processed with trim-galore (‘Babraham Bioinformatics - Trim Galore!”) to remove adaptors and low quality sequences. Processed reads were mapped to release six reference D. melanogaster genome () or release two reference D. simulans genome (), using bwa mem with default parameters (v 0.7.5) (). Reads with mapping quality score lower than 30 were filtered using samtools () and excluded from further analysis. We used Macs2 with a liberal significance threshold (p=0.2) to generate peak calls for IDR (irreproducible rate) analysis (), which evaluates the reproducibility of ChIP replicates. Replicates for our samples had low IDRs ( and ), and were combined to generate a single H3K9me2 fold enrichment track (between IP and matching input) for each sample. Our analyses were based these fold-enrichment tracks., The baseline H3K9me2 enrichment level is slightly different between the two D. melanogaster strains, potentially due to technical and/or biological reasons. As the enrichment of repressive epigenetic marks is generally confined to 10 kb from TEs (), we used the H3K9me2 enrichment levels 20–40 kb upstrea […]

Pipeline specifications

Software tools Trim Galore!, BWA, SAMtools, MACS
Organisms Drosophila melanogaster, Toxoplasma gondii, Drosophila simulans