RNA star with reference genome from history error

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1

Hi,

Apologies if I don’t manange to explain my problem very well I am quite new to analysising sequencing data.

I have a new assembly and annotations in my galaxy account and wanted to align samples with RNA-star, then run a DESEQ2 analysis. I have previously done this using an old assembly and annotations with no issues. However when I run my grouped samples with new genome and annotations i get the below error for all samples.

STAR --runMode genomeGenerate --genomeDir tempstargenomedir --genomeFastaFiles refgenome.fa --sjdbOverhang 149 --sjdbGTFfile /data/dnb09/galaxy_db/files/d/0/0/dataset_d004b7ff-5d34-43e9-80c4-b0ff4bedace3.dat --genomeSAindexNbases 14 --runThreadN 10 --lim

Any help would be greatly appreciated.

Cheers

Toby

2

Hi @Toyle1

The message you posted back is the command line for the tool. Much of the content is abstracted, so it doesn’t provide enough information to diagnose what might be going on content-wise.

First, try a rerun to eliminate some technical server-side issue.

Then, examine your reference genome and reference annotation. Is the formatting Ok? Is the content a match between the files, other inputs, and any feature/attribute settings on the tool form?

I added some tags to your post, and these are the most relevant FAQs

The above solves most technical errors. If you need more help, please share back more information. Troubleshooting errors && What information should I include when reporting a problem?