I am trying to use RNA STAR to map my single end RNA seq reads.
I am trying to use reference genome from history and to make a temporary index by uploading:
- caenorhabditis_elegans.PRJNA13758.WBPS14.genomic.fa.gz as a ref. genome
- caenorhabditis_elegans.PRJNA13758.WBPS14.annotations.gff3 as a annotation file
These are downloaded from the: https://parasite.wormbase.org/Caenorhabditis_elegans_prjna13758/Info/Index/
It starts running the STAR, everything seems OK, but at the end I get empty files (0 bytes BAM file) and a message: An error occurred setting the metadata for this dataset
Set it manually or retry auto-detection
I cannot report the bug because it is labeled as if it was working fine (its green).
Inside the BAM file it is written: Could not display BAM file, error was:
file has no sequences defined (mode=‘rb’) - is it SAM/BAM format? Consider opening with check_sq=False
I have tried to upload annotation file for C. elegans from Ensemble, but Galaxy does not allow me to select that gtf file, although it is uploaded into history.
Does anyone has some suggestion how to get a normal BAM file?