ERANGE problems!

[gthomas]

Hi,

I'm new to RNA-seq and am trying to use ERAGNE to map reads to the mouse genome using Bowtie v0.10.0. I've got my alignment and have created and indexed my .rds file from this. When I run the runStandardAnalysis.sh script it finishes in ~5 minutes with no RPKM values... very little appears to happen at the geneMrnaCounts.py, which completes almost instantly :-

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runStandardAnalysis.sh mouse BTG1 ../RepeatMask/mm9.fa.out
runStandardAnalysis.sh: version 3.6
running with settings: mouse BTG1 ../RepeatMask/mm9.fa.out
psyco not running
/software/caltech/ERANGE/geneMrnaCounts.py: version 4.7
marking NM
caching ....
dataset BTG1.rds
metadata:
bowtie_mapped True
dataType RNA
paired True
rdsVersion 1.1
readsize 51

4983482 unique reads, 1003996 spliced reads and 674478 multireads
default cache size is 10000000 pages
found index
getting gene features....
getting geneIDs....

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As you can see, no gene features or IDs are imported at this point, should they be? Does anybody have any idea what may be causing my problems?

Cheers,
Graham

[gthomas]

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