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In the last step, though I provided the "blast_pairs.gene_ " file, this step ran again and generated a similar file ref_6.genesym.gz,ref_6. prep_genome_lib.pl -genome_fa -gtf ucsc.hg19_star.gtf -blast_pairs blast_pairs.gene_ -CPU $SLURM_CPUS_PER_TASK -pfam_db. Makeblastdb -in cDNA_seqs.fa.masked -dbtype nuclīlastn -query cDNA_seqs.fa.masked -db cDNA_seqs.fa.masked \įusionFilter/util/ blast_outfmt6_replace_trans_id_w_gene_ cDNA_seqs.fa blast_pairs.outfmt6 | gzip > blast_pairs.gene_ RepeatMasker -pa $SLURM_CPUS_PER_TASK -s -species human -xsmall cDNA_seqs.fa But only blastn ran in my situation.Ĭould you please point me in the right direction.įollowed the wiki document in FusionFilter.wiki directory and did the following stepsġ. In this link I can see that repeatmasker and blastn is run within the. Could this be the reason for such huge change.? ![]() repeatmasking did not happen and directly blastn started. ![]() I looked into the pipeliner.cmds that is generated while running prep_genome_lib.pl. I used the same STAR mapping parameters specified on your github page and generated file to run STAR-fusion. I don't understand the reason for such huge change. new/AnnotFilterRule.pm -pfam_db -CPU $SLURM_CPUS_PER_TASK -output_dir star_fusion_indexĪfter running STAR-fusion only 54 fusions genes were predicted for the same sample. prep_genome_lib.pl -genome_fa -gtf ucsc.hg19_star.gtf -fusion_annot_lib. Pfam-A.hmm -CPU $SLURM_CPUS_PER_TASK -output_dir new prep_genome_lib.pl -genome_fa -gtf ucsc.hg19_star.gtf -pfam_db. I followed the steps in fusionfilter and ran the following steps I am trying to add STAR_fusion to my genomics pipeline and hence wanted to build STAR-fusion index for hg19 reference that is already being used in our pipeline. 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