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We assessed the quality of the assemblies based on the total number of transcripts, open reading frames predicted using Transdecoder and highest mapping percentage of the reads using GSNAP.
23 26 After listening to interviews and reading the transcripts to become familiar and get a sense of the whole, two researchers independently analysed and coded a subset of transcripts (open coding) using a mixed-methods research software.
After listening to interviews and reading the transcripts to become familiar and get a sense of the whole, two researchers independently analysed and coded a subset of transcripts (open coding) using a mixed-methods research software [ 24].
To assess the protein coding potential of unannotated transcripts, open reading frames were identified and translated using the 'getorf' program, part of the EMBOSS suite of sequence analysis software [ 78].
Analysis comprised three stages: (1) initial categories were created based on review of transcripts (open coding); (2) interconnections between categories were generated (axial coding); and (3) hypotheses regarding the interconnections between categories were proposed (selective coding) [ 28].
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Identification and sequence information for many lncRNAs and other novel transcripts opens the possibility to study their transcriptional responses and begin to explore their biologic function in An. gambiae using functional assays such as dsRNA gene silencing.
The transcripts opened a window into dementia, incontinence and the rages of the dependent elderly, as well as "the petty annoyances that usually occur when people are forced into close proximity with one another," Dr. Hartog said.
In addition to these technical attributes, RNA-seq data can be used to detect gene mutations, splice variants, and fusion transcripts, opening up new avenues of study.
Of the ~54,000 probesets on the Affymetrix U133 plus 2.0 array, about 36,000 were analyzed after filtering out the probesets targeting non-annotated transcripts, opening reading frames and hypothetical genes.
Site-specific RNA-editing events in transcript open reading frames that generate new isoforms of encoded proteins represent the best-understood mechanism of ADAR action.
However, whereas the PMEPA1-001 transcript open reading frame and a part of the intergenic promoter region are highly conserved through evolution, this seems to be true to a lesser degree for NKILA equivalent transcripts (Supplementary file S1 and discussion therein).
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