Each interviewee was given the opportunity to review their transcript in order to correct errors or add information; no substantial changes were requested.
Participants were given the transcript of their interview to correct any misunderstanding and add any omissions.
This information, provided in conjunction with commonly available changes in p-value and determination of transcript presence, may serve to correct for technical variability in array experiments performed without replication.
Thus, co-transcriptional recruitment of the THO/TREX complex to the nascent mRNA of intron-containing transcripts ultimately leads both to correct 3′-end processing and to recruitment of (among other proteins) Yra1p, which in turn recruits the Mex67p- Mtr2p heterodimer (reviewed in Rodriguez-Navarro and Hurt 2011).
To correct for transcript length and depth of coverage, raw reads were converted into reads per kilobase of exon per million mapped reads (RPKM) [ 23].
Short read and/or assembled transcript alignments are typically used to correct the coordinates of intron-exon boundaries in existing gene annotations or predictions [ 7], to train gene predictors [ 8], and can also be incorporated directly into gene prediction by hybrid gene predictors [ 9, 10].
All gene predictions were provided as input to the Apollo genome annotation editor (version 1.9.3, [ 105]), and genes included in phylogenetic analyses were manually checked against transcript information generated by Cufflinks to correct for 1) missing genes, 2) partial genes, and 3) separated genes.
The participant was asked to correct or annotate the transcript and return it; all changes were accepted.
Additionally, we asked the interviewees to correct and approve the transcripts so that we could use them for our study.
To detect potential alternative splicing events, we obtained 252,484 high-fidelity Chlamydomonas EST sequences that Liang et al. corrected using cDNA termini to anchor transcripts to their correct positions in the genome [ 20].
