I have used genome of Mentha longifolia in NCBI as a reference genome but unfortunately when I write the command line for RSEM analysis, the following error is shown.
tnx
command line:
rsem-prepare-reference –gtf annotation.gtf
--bowtie2
--bowtie2-path /path/….
/path/genome.fna
/patg/output-ref
Error:
Gtf file might be corrupted.
Stop at line: t’Y
Error message: strand is neither + nor –
Hi, I don't know if it will fix the problem but it's looks like you have "-gtf", try "--gtf".
Somaye Shams
1. Please check the names of chromosomes in both genome and annotation file.
2. Open the annotation file in text editor and check it in the last line whether a complete file or not?
Somaye Shams
Download genome and annotation file again. Send link, from where you downloaded genome and annotation file.
Dear Suresh This is the annotation file link but this file has a problem. ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/642/375/GCA_001642375.1_Mlong1.0/GCA_001642375.1_Mlong1.0_genomic.gff.gz I sent an email to the author and she sent the annotation file to me in gtf format. But unfortunately, this file also has problems.
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