Thirdly, the publication bias were observed, however, we used trim-and-fill method to correct the bias, which did not obviously alter the positive association.
We used trimmed EST length as transcript length.
Adaptor and quality trimming was performed using Trim Galore! v0.3.5.
Adapter removal was performed using Trim Galore! version 0.4.5 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).ac.uk/projects/trim_galore/
Using trim cuts, damaged surface layer can be removed and surface integrity can be improved significantly (Jangra 2012, 2014; Sakar et al. 2008; Sanchez et al. 2007).
Adapter and windowed adaptive quality trimming was performed on the raw reads (using Trim Galore).
Publication bias was examined by visually examining the filled funnel plots using trim and fill method.
Samples that have technical replicates were integrated into a single file and trimmed by using Trim Galore [ 23].
We found switches in line origin probabilities for 88% of these using triM and 53% using GridQTL.
