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. I ran STAR-fusion by downloading the prebuilt CTAT library from for GRCH37_v19 and 185 fusion genes were predicted.
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