Question: Star-Fusion last-matching gene pairs file
0
gravatar for yelekley7
3 months ago by
yelekley70
yelekley70 wrote:

Hello,

Could you please clarify the correct file to use as a last-matching gene pairs file for Star-Fusion. I ran human exome RNA-seq data through Star within Galaxy and would like to continue analysis with Star-Fusion.

I'm looking for hg19 fusions but not sure which of the files 'plug-in-play' or 'source-data' to download and upload to galaxy for analysis. Could you please specify the exact file I need to use. The 'source-data' folder contains numerous files including:

ref_genome.fa, CTAT_HumanFusionLib.v0.1.0.dat.gz ref_annot.gtf

Here is the location of the CTAT files: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/

Thanks

rna-seq star input fusion • 150 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by yelekley70
1
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Updated reply

The file within the 'source-data' archive ref_annot.cdna.allvsall.outfmt6.toGenes.sorted.gz contains the gene-to-gene mapping.

The reference genome fasta and annotation GTF from this source should probably be used for all steps (including STAR mapping) in the analysis to make sure inputs are consistently based on the same underlying genome build/annotation.

Blastn with 12-column tabular output created by mapping the exome fasta against itself will also create the gene-to-gene data. Use this method for custom genomes/non-human genomes.

Thanks! Jen, Galaxy team

Cross-posted at https://www.biostars.org/p/310047/

ADD COMMENTlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson25k

I keep getting an error: "This job was terminated because it used more memory than it was allocated". Is there anything I can do? Thank you very much for your help.

ADD REPLYlink written 3 months ago by yelekley70

This most likely means that the job actually exceeded resources at https://usegalaxy.org. I've already asked our administrator today if we should consider increasing the resources given to this tool and no decision has been made yet.

Input content/format can also trigger memory failures. This is how to check: https://galaxyproject.org/support/tool-error/

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson25k

Thanks Jennifer, The same files processed successfully with STAR-RNA, therefore, it must the be memory allocation issue. Please let me know when the decision is made to add more memory. I need to know if I should look for another way to process the files. Thanks again.

ADD REPLYlink modified 3 months ago • written 3 months ago by yelekley70

Follow this ticket for updates: https://github.com/galaxyproject/usegalaxy-playbook/pull/107

Meanwhile, the tool could be used on your own local, docker, or cloud Galaxy.

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson25k
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