I used RSEM to map RNA-seq data and calculate gene expression, but there were some errors when I tried to prepare reference sequence by using rsem-prepare-reference program. My operation as follows:
$ rsem-prepare-reference --gtf genes.gtf genome.fa oil_palm
Then the error which pasted here was shown in terminal:
Stop at line: EG5_Chr1 GlimmerHMM CDS 6237 6344 . + 0 Parent=p5_sc00105.V1.gene434 (This is the first line of my gtf file)
Error message: Cannot separate the identifier from the value for attribute Parent=p5_sc00105.V1.gene434
I don't know how to solve it, so I ask for your help.
Notes: My data (eg. gtf file and genome fasta file) were downloaded from oil_palm genome website: http://genomsawit.mpob.gov.my/genomsawit/auth/index.php?track=12