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Reads were initially filtered against sequencing adaptors and barcodes and a collection of published A. niger rRNA sequences prior to read mapping.
Prior to read mapping, raw reads were initially characterized with FastQC (http:// http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) and were trimmed to remove ambiguous and low quality reads with Trimmomatic v0.32 [ 43].
Reads were quality-trimmed using the default settings of ConDeTri [ 39] prior to read mapping and transcript quantification with the Cufflinks pipeline (Bowtie 1.0.0, TopHat 2.0.9, Cufflinks 2.1.0) and the peach v1.0 reference genome [ 25, 40].
Prior to read mapping, we trimmed low-quality ends and discarded reads reduced to fewer than 20 bases using Sickle (https://github.com/najoshi/sickle, last accessed July 30 , 2013.
We used the GTF gene model file provided by The Sanger Centre for splice junctions and read counts (ftp://ftp.sanger.ac.uk/pub/users/searle/cat). Each file was sorted using novosort (http://www.novocraft.com/wiki/tiki-index.php?page=Novosort&structure=Novocraft+Technologies&page_ref_id=91) prior to read counting.
Prior to read mapping, 3′ poly(A) sequences likely to be derived from the mRNA poly(A) tail were trimmed using a procedure that tolerated some amount of sequencing error: we computed a score s i for each position i in the read which was equal to the sum of the quality scores of each A after position i minus three times the sum of the quality scores of each non-A after position i.
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