i have a RNA-seq data, i want to analyze the differential expression, i have finished fastqc+hisat2+stringtie+stringtie merge, now i need to identificate lncRNA, there are the principles: (1)Transcripts with one exon and shorter than 200 bp were removed; (2) The reads coverage of transcript was calculated using Stringtie (1.2.4), and those with reads coverage less than 3 were eliminated; (3) Transcripts belong to coding-genes, pseudogenes, pre-microRNA, tRNA, rRNA, and snoRNA were removed; (4) Protein coding potency of transcripts were calculated by three software: Coding-Non-Coding-Index (CNCI)47 (score < 0), Coding Potential Calculator (CPC)48 (score < 0), and Pfam-scan49 (E-value < 0.001). Transcripts identified with coding potential in any of the three tools were filtered out. for (2) and (3), what should i do
you already described pretty well what to do.