Question: RNA Star problems
gravatar for fraheto
17 days ago by
fraheto10 wrote:

I am pretty new in Galaxy. I have been following some tutorials in order to perform some DEG with my data( 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:

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, 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?


ADD COMMENTlink modified 16 days ago by Jennifer Hillman Jackson25k • written 17 days ago by fraheto10
gravatar for Jennifer Hillman Jackson
16 days ago by
United States
Jennifer Hillman Jackson25k wrote:


The annotation needs to have chromosome identifiers that are a match for the genome used for mapping.

Try the GeneCode Genes GTF version of the annotation.

Full details are in this prior Q&A, including where to source the GTF and FAQs about how to detect and correct format/chromosome mismatch problems:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 16 days ago by Jennifer Hillman Jackson25k

Thank you so much. I will try it again taking into account your advices

ADD REPLYlink written 16 days ago by fraheto10

It worked perfectly. Thank you so much

ADD REPLYlink written 15 days ago by fraheto10
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