brianjohnhaas
commented
4 years ago Hi,
You'll need to set the --genome_lib_dir parameter to your /path/to/your/ctat_genome_lib/
or you can set the env var CTAT_GENOME_LIB to this path instead for convenience - useful if you're using other CTAT tools that leverage it.
best,
~b
On Thu, Feb 13, 2020 at 1:06 AM Arpitm notifications@github.com wrote:
i am trying to run TrinityFusion, to identify putative integration site for transgene. This is my command "perl ../TrinityFusion --left_fq reads_1.fq.gz --right_fq reads_2.fq.gz --chimeric_junctions Chimeric.out.junction --aligned_bam Aligned.out.bam --genome_lib_dir ../../../Trinity_fusion/ctat_genome_lib_build_dir" but i am getting this error "Use of uninitialized value $ENV{"CTAT_GENOME_LIB"} in concatenation (.) or string at ../TrinityFusion line 46." I am novice to perl so may be this is some silly issue but can you have a look in to this
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
i am trying to run TrinityFusion, to identify putative integration site for transgene. This is my command "perl ../TrinityFusion --left_fq reads_1.fq.gz --right_fq reads_2.fq.gz --chimeric_junctions Chimeric.out.junction --aligned_bam Aligned.out.bam --genome_lib_dir ../../../Trinity_fusion/ctat_genome_lib_build_dir" but i am getting this error "Use of uninitialized value $ENV{"CTAT_GENOME_LIB"} in concatenation (.) or string at ../TrinityFusion line 46." I am novice to perl so may be this is some silly issue but can you have a look in to this