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MINASM=9
test: forward_reverse stripped
regular:
${TRINITY_HOME}/Trinity --left reads.left.fq.gz --right reads.right.fq.gz --seqType fq --SS_lib_type RF --CPU 2 --max_memory 1G --output trinity_outdir --output trinity_regular_outdir --no_cleanup
${TRINITY_HOME}/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl --query trinity_regular_outdir.Trinity.fasta --target ${TRINITY_HOME}/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/refSeqs.fa --no_reuse
./ensure_min_asm.pl ${MINASM} trinity_regular_outdir.Trinity.fasta
forward_reverse:
${TRINITY_HOME}/Trinity --left reads.ForRev_1.fastq.gz --right reads.ForRev_2.fastq.gz --seqType fq --SS_lib_type RF --CPU 2 --max_memory 1G --output trinity_ForwRev_outdir --no_cleanup
${TRINITY_HOME}/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl --query trinity_ForwRev_outdir.Trinity.fasta --target ${TRINITY_HOME}/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/refSeqs.fa --no_reuse
./ensure_min_asm.pl ${MINASM} trinity_ForwRev_outdir.Trinity.fasta
stripped:
${TRINITY_HOME}/Trinity --left reads.left.stripped.fq.gz --right reads.right.stripped.fq.gz --seqType fq --SS_lib_type RF --CPU 2 --max_memory 1G --output trinity_stripped_outdir --no_cleanup
${TRINITY_HOME}/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl --query trinity_stripped_outdir.Trinity.fasta --target ${TRINITY_HOME}/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/refSeqs.fa --no_reuse
./ensure_min_asm.pl ${MINASM} trinity_stripped_outdir.Trinity.fasta
clean:
rm -rf ./trinity*outdir
rm -f ./trinity*outdir.Trinity.fasta*
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