I have Total RNA TrueSeq Illumina Stranded library (human). My goal is to find novel (and non-novel) non-coding transcripts in my data (experimental vs control).

After a LOT of Google-fu and asking questions on this website, this is the methodology that I am currently using - 

1. Align the fasta files with STAR to hg38
2. Assemble transcripts for each sample, merge transcripts from all samples (to get a unified transcriptome that represents all the samples), and estimate transcript abundances - all using Stringtie (protocol paper - https://www.nature.com/articles/nprot.2016.095#procedure)
3.  Use tximport to infer integer counts from the Stringtie transcript abundances and export it to DESeq2.

I wanted to know if this methodology makes sense. Is there anything for which a better method makes more sense.
I hope my question is not too broad, given that I do specify the exact pipeline I am employing :) 

Hi, you can follow the below given pipeline for complete analyses

1. Algin reads to the genome using the STAR (Already completed)
2. Run stringtie to assemble transcripts with default parameters which (filter out transcript below 1 FPKM)
3. Merge all transcriptome assemlby into 1 merged assembly ( stringtie --merge)
4. Extract protein coding genes in gtf format from ENSEMBLE GTF
5. Download already known noncoding RNAs ( ENSEMBLE + LNCIPEDIA)
6. Merge all known noncoding annotation in to 1 gtf file by ( using cuffmerge)
7. gffcompare the protein coding and all knonw protein codng gtf to your assembled merged gtf file. 
8 Extract the classes "u", "i" and "X" with bash script (For more details check gffcompare classes.)

9. Now extract the MSTRG id and extract gtf file for this using the grep or something. 
10 Extract fasta file for novel noncoding using gffread
11. Filter the transcript wiht length less then 200 and single exons transcript. 
12. Use CPAT and PLEK to predit the coding potenial for the novel transcripts using the transcript sequence. 
13. Further filter the the transcritp by using NCBI blast with known protein homology based ( use only 3 frames)
14. This would be your final list for the transcripts.
15 Rerun the stringtie with -e -B option to get count in FPKM, Coverage and TPM. 

16 Run DESEQ2 For differential expression 

17. Annotate the novel transcript by looking into near by genes by bedoops closet tool.
18. Further find out signifigance by creating the corrleation beteween protein coding and your novel transcripts. 

19 Gene enrchimnent anlaysis of the near by genes and protein coding gens for understaing mechanism
