Yes I have successfully used lifescope for mouse genome small RNA mapping. What version of miRBase were you trying to incorporate? We never updated ours after setting it up for miRBasev18.
If you are still having troubles I could send you the mouse input files we successfully used? In the meantime I'll find some time to update our system to miRBasev19 to see if it works on our end.
Cheers
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Lifescope smallRNA module with mouse genome
Has anybody had any luck in running in smallRNA module for Lifescope for mouse genome. ?
I've been using the input files I downloaded from mirbase (miRNA.txt for mature, mmu.gff2/mmu.gff3 for precursor) . Lifescope fails with the following error.
secondary-mm9-smallrnamapping [2%] [JOB_FAILURE] Error in generating miRBase invocation command. Pipeline Exception Could not find any precursors in the genome reference file. Input GFF file /data/LifeScopeDisk/referenceData/external/mm9/mirbase/mmu.gff and the input reference file /data/LifeScopeDisk...............
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