The rationale behind this task was that we wanted to ensure comparable processing demands for reading material and nonreading material, as well as for words and pseudowords with as little top-down influence as possible.
There is a long history documenting the processing requirements for reading different types of English words (Coltheart 1981; Seidenberg and McClelland 1989; Paap and Noel 1991; Plaut et al. 1996).
Given that length effects are interpreted by advocates of dual-route models as evidence of serial processing this would seem to pose a serious challenge to models of single word reading which postulate a common parallel processing mechanism for reading both words and nonwords (Coltheart, Rastle, Perry, Langdon, & Ziegler, 2001; Rastle, Havelka, Wydell, Coltheart, & Besner, 2009).
In the study of Hirst et al., even though the tasks both involved verbal stimuli, it is plausible that dictation may rely more on an automatic phonological store while the semantic processing needed for reading comprehension relied primarily upon a central attention resource.
The remaining sequences were used for further characterization (see Additional file 1 for flow chart of the procedure for processing of reads).
After removing adaptor sequences and filtering out low quality data (see Additional file 1 for flow chart of the procedure for processing of reads), we obtained small RNAs with size range of 10-30 nt, with an enrichment in 20-22 nt.
Trimmomatic includes a variety of processing steps for read trimming and filtering, but the main algorithmic innovations are related to identification of adapter sequences and quality filtering, and are described in detail below.
The error rates reported for Sanger sequencing vary from 0.001% [ 13, 18] to more than 1% [ 19, 20] and seem to depend on the software that is used for post processing of reads.
Therefore, Kmerspectrumanalyzer is sufficiently robust against sequencing error to negate any need for the pre-processing of read data for error mitigation.
An alternative view is articulated in connectionist models of reading (Harm & Seidenberg, 1999, 2004; Plaut et al., 1996; Seidenberg & McClelland, 1989) which assume that a single parallel processing mechanism is responsible for reading both words and nonwords.
More critically, if specialisation for reading is at the level of neuronal populations that overlap with object processing areas, then evidence for reading specific responses in left OT will require single cell recordings or techniques with much higher spatial resolution than fMRI.
