I am trying to estimate the abundance of transcripts using Trinity's Estimating Transcript Abundance. I have noticed that for some transcripts I am getting an expected count of 0. I am unsure how to interpret this result. Is this number low and just being rounded down?
Link to my output: https://ibb.co/mHdFKX8 (Couldn't see how to insert a table in this post)
Prior to this I map the paired raw reads to the host genome to capture the unaligned as I am interested in viruses. I then run Trinity on the unaligned reads.
My estimate abundance code:
/path/align_and_estimate_abundance.pl --transcripts file.trinity.Trinity.fasta --seqType fq --left unaligned_fastq.1 --right unaligned_fastq.2 --thread_count 56 --est_method RSEM --aln_method bowtie --trinity_mode --output_dir abundance --prep_reference