I am pretty new in Galaxy. I have been following some tutorials in order to perform some DEG with my data( https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html). Everything seems to be easy, however I am getting problems. I am trying to alinng single-ends reads from Illumina as follow:
Single-end or paired-end reads: Single-end reads in my history. Custom or built-in reference genome: Use a built-in index. Reference genome with or without an annotation: Use genome reference without builtin gene-model. Select reference genome: Mouse (Mus musculus):mm10. Gene model (gff3,gtf) file for splice junctions: ftp://ftp.ensembl.org/pub/release94/gff3/mus_musculus/Mus_musculus.GRCm38.94.gff3.gz. I launch the program but sooafter I get this message: This job was terminated because it used more memory than it was allocated.
I have tried to download the mouse genome from ENSMBL ftp://ftp.ensembl.org/pub/release-94/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz, and select it to perform the alinment instead of Mouse (Mus musculus):mm10 in your database, but this time i get the mesasage: Fatal error: Matched on FATAL ERROR Fatal INPUT FILE error, no valid exon lines in the GTF file: /galaxy-repl/main/files/028/060
I have tried to transform Mus_musculus.GRCm38.94.gff3 file to gtf with gffread tool, since gft3 file from ENSEMBL is not recognized by RNA star. I have also tried to use mmu.gff3 file from miRbase (my reads come from small RNA libreries) and I get the same problem.
Could you be so kind to hellp me?