I have paired end Illumina highseq 2000 data from non model organism. I did denovo assembly with Trinity. Trinity assembly generated around 1.5 million transcripts. Then I align the read to the transcriptome with the help of bowtie2 and bam file has been generated. Now I would like to do transcript abundance estimation via alignment based RSEM method.

I follow the instrusction from the Trinity transcript quantification mannual. I tried to prepare the reference for alignemt with the following script and it gives me the error

 "Mapping Info is not correctt, cannot find TRINITY_DN134574_c1_g1_i12's gene_id!"

the script I used for this is:

/home/trinityrnaseq-2.2.0/util/align_and_estimate_abundance.pl --transcripts ~/nobackup/trinity_a2b2_seq_111016_1333/Trinity.fasta  --est_method RSEM --aln_method ~/nobackup/trinity_a2b2_seq_111016_1333/bowtie2.nameSorted.bam  --trinity_mode --thread_count 30 --prep_reference --output_dir ~/nobackup/trinity_a2b2_seq_111016_1333/RSEM/rsem_outdir

Could you please guide me what I did wrong and how can I fix it.

Thanks