I am indexing the genome and it runs to completion
gedi -e IndexGenome -s ./genome/GCA_GRCh38_noALT_fusions.fa -a ./genome/annotations/stringtie_fusion.sorted.gtf -nomapping
However when I try to call ORFs the genome cannot be found
gedi -e Price -reads /gstore/scratch/u/malekose/riboseq/stringtie_fusion/merged_Aligned.out.bam -genomic stringtie_fusion.sorted -p
...
Error:
Genomic name stringtie_fusion.sorted does not exisit in config/genomic!
According to these instructions there should be an oml file created in $HOME/.gedi/genomic, but that is not the case for me:
ls -lah $HOME/.gedi/
drwxr-xr-x 2 malekose idmgmt 8.0K Aug 7 09:06 .
drwx------ 21 malekose idmgmt 8.0K Aug 6 16:59 ..
-rw-r--r-- 1 malekose idmgmt 2.6K Aug 7 09:06 gedi0.log
What can I do, I have tried specifying the full path to the index, but nothing seems to work.
I am indexing the genome and it runs to completion
gedi -e IndexGenome -s ./genome/GCA_GRCh38_noALT_fusions.fa -a ./genome/annotations/stringtie_fusion.sorted.gtf -nomappingHowever when I try to call ORFs the genome cannot be found
According to these instructions there should be an oml file created in $HOME/.gedi/genomic, but that is not the case for me:
What can I do, I have tried specifying the full path to the index, but nothing seems to work.