Hi there!
I am working with human RNA-seq data from previous publications and I am trying to replicate the results, obtained through R in these publications, with galaxy.
Specifically, I am having problems with the alignment process.
I have previously been working with the GRCh38.87 genome annotation through RNA STAR to align my reads, and so far has worked well with the human GRCh38 built-in index in galaxy.
However, when I try to replicate the analyses uploading the GRCh38.79 using this URL: “ftp://ftp.ensembl.org/pub/release-79/gtf/homo_sapiens/”, and using the “Homo_sapiens.GRCh38.dna.primary_assembly.fa” file downloaded from this URL: “Index of /pub/release-111/fasta/homo_sapiens/dna” I find that even though RNA STAR runs the job, the output “.bam” file does not produce any data.
In fact said file states: “Could not display BAM file, error was:
file does not contain alignment data”
Has anyone else found themselves in this situation? Am I using the wrong gtf and fasta files for acquiring alignment files, or is it a problem with the generation of a new index?
Thank you very much in advance,
Coral