About COSMIC fusions

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小林賢子

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Jun 18, 2024, 8:37:32 PMJun 18

to Trinity_CTAT_users

Dear Dr. Haas,

Always thank you very much.

I am trying to get COSMIC fusions.

I added the option --predict_cosmic_like. However, unsuccessful.

Command and error message are below.

user@localhost:~/STAR-Fusion$ docker run -v `pwd`:/data --rm trinityctat/starfusion STAR-Fusion --left_fq /data/U-937_1.fastq.gz --right_fq /data/U-937_2.fastq.gz --genome_lib_dir /data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir -O /data/StarFusionOut --FusionInspector validate --examine_coding_effect --denovo_reconstruct --predict_cosmic_like
Error, don't understand arguments: [--predict_cosmic_like] at /usr/local/src/STAR-Fusion/STAR-Fusion line 498.

I confirmed there was no problem in operation without the option --predict_cosmic_like.

Could you tell me some solution?

Tetsuko Kobayashi in Japan

Brian Haas

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Jun 19, 2024, 10:08:21 AMJun 19

to 小林賢子, Trinity_CTAT_users

Hi,

It doesn't look like there's a pass-through option for this in STAR-Fusion, and so you'll want to run FusionInspector directly and separately with that option.

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