Error about rsem-prepare-reference

Question

[Ginsea Chen]

Hi ALL

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.

[nash.claire]

Hi I'm wondering whether you solved your problem as I'm having the same problem now. I've checked my gtf file against the link from Bo Li and my gtf seems absolutely fine so not sure what else the problem can be....

Answer 1

[bli25]

Hi Ginsea,

I doubt if the file you have is in GTF format. Please refer http://mblab.wustl.edu/GTF22.html for the format RSEM uses.

Best,
Bo Li