I am trying to align my rna seq data using RNA STAR and the GTF file i downloaded from NCBi. I tried a file from Genecode as well. The links are below
I keep getting the same error message:
‘’'Fatal INPUT FILE error, no valid exon lines in the GTF file: /data/dnb03/galaxy_db/files/2/f/f/dataset_2ff93edb-4e10-47af-8a34-4a2262379bde.dat
Solution: check the formatting of the GTF file. One likely cause is the difference in chromosome naming between GTF and FASTA file.
Feb 09 20:06:52 … FATAL ERROR, exiting’’’
I tried both gtf files. I made sure they were unziped before uploading. I tried removing the first 4 lines which are comments.
I was using the genome file provided by Galaxy for sars cov-2 but it doesnt have an attached gtf file so i was importing these. I am using the galaxy.eu server
The same RNA seq files I was able to align with RNA STAR to the human genome (hg19) from (http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/hg19.refGene.gtf.gz) which I found on this support thread (Help for Differential Expression Analysis).
When I look at the begining of the files both the human and the covid file look the same (after i removed the comment lines). The third line in both files is “features”
Any help is appretiated!