The purpose of this study was to detect the lncRNA content in various organs of Nymphaea minuta
Materials and methods
lncRNA is a long non-coding RNA with a fragment length greater than 200nt. According to the structure and non-coding characteristics of lncRNA, we screened candidate lncRNA through strict three-step screening conditions. Follow-up analysis was performed on the genes and the candidate lncrnas that were rigorously screened.
First, we use Stringtie software to assemble transcripts using the comparison results of Hisat2. After the transcripts with uncertain chain orientation are removed, lncRNA is screened from the remaining assembled transcripts.
1) Animals: transcripts with screening length >=200bp and exon number >=2; Plant: Screening length Screening length >=200bp;
2) Filter transcripts whose Class_code is x/u/i. That is, Anti-sense LncRNA, Intergenic lncRNA, Intronic LncRNA transcripts. (Where x refers to exons covering the reference transcript on the antichain of the reference transcript's chain; u refers to the unknown transcript, in the intergenic region; i means entirely in an intron of the reference transcript);
3) Screening lncrnas with coverge > 3 in at least one sample. That is, it appears at least three times in the transcript of one sample.
