Fig. 1

Overview of the transcriptome generated by PARS. a. Venn diagram representing paired and unpaired positions at 24 hpf zebrafish transcriptome obtained from PARS data. Approximately, 3.4 million positions are jointly obtained in both V1 and S1 cleaved samples. Blue (V1) and the green (S1) ellipse display positions with ratio score > 1, termed as peaks. Of these, 186,306 positions are overlapped peaks showing ambiguous positions. b. A total of 54,083 transcripts were assembled, from which 25,158 transcripts have positions with overlapping peaks in both V1 and S1 dataset. Amongst these 11,450 transcripts had more than 5 positions overlapping and are categorised as multi-conformation transcripts. c. Abundance of transcripts based on per base structure coverage. Coverage of the total transcripts (54,083) was estimated by the number of reads relative to the positions covered and the length of the transcript. Most of the transcripts (46,173) were less than 40% covered, 7366 transcripts were 40–85% covered, while 544 transcripts were > 85% covered. d. Bar plot representing the biotype of 54,083 transcripts. The biotype of the transcripts is represented. The inset pie shows distribution of transcripts with > 85% covered based on the function. PC: protein coding, lncRNA: long non-coding RNA, NMD: non-sense mediated decay, rRNA: ribosomal RNA, Misc: miscellaneous