I had posted this issue previously in a number of forums, but could not find a way out. I am interested in a gene_level analysis (not interested in novel genes/isoforms)
I have ran the StringTie tool thrice with the following commands:
stringtie -p 4 -G transcripts_exon_for_analysis.gtf -o test_out.gtf accepted_hits.bam stringtie --merge -p 4 -G transcripts_exon_for_analysis.gtf -o rice_merged.gtf mergelist.txt stringtie -e -B -p 4 -G rice_merged.gtf -o ballgown/root_rep1/root_rep1.gtf root1_rep1.bam
After this I have used prepDE.py to obtain the gene_count matrix which is an input for DeSeq. Most of my IDs in the matrix are StringTie IDs, Majority of the genes in the annotation file are not picked up. Is there a way I can map the IDs back to my annotation file ?
Also, can I use featureCounts R package to get a gene count matrix incase StringTie doesnt work? I am not interested in novel genes/isoforms