Intron Retention data (using iDiffIR)

Intron retention data for Collins et al. 2019This contains data for 3 mutant lines from the mouse DMDD project (Dhx35, Morc2a and Hmgxb3).Repeat annotation identified by RepeatMasker was downloaded (http://www.repeatmasker.org/genomes/mm10/RepeatMasker-rm405-db20140131/mm10.fa.out.gz) and filtered to remove repeats marked as Simple_repeat or Low_complexity.In order to reduce potential mapping bias, FASTQ files were realigned to the GRCm38 reference genome using TopHat259 (v2.0.13, options: --library-type fr-firststrand), but without a transcriptome reference.Counts for repeats were produced using htseq-count61 (v0.6.0 options: --stranded=reverse). Intronic retention was examined using iDiffIR (https://bitbucket.org/comp_bio/idiffir)