brianjohnhaas
commented
1 month ago Hi,
It's probably because in your data, the chromosome value is '7' instead of 'chr7'. It expects that you're using our CTAT genome library for running STAR as part of STAR-Fusion.
hope this helps,
Brian
On Fri, Sep 27, 2024 at 7:23 AM Chih-Fan Chang @.***> wrote:
Hi,
I am trying to use ctat-splicing to detect METexon14 skipping but it doesn't seem to work. In the "prefix.introns" file, I do see the variant. However, it does not appear in the "prefix.cancer.introns" file.
This is the record in the ouput "prefix.introns" file: 7:116771655-116774880 + MET^ENSG00000105976 14 0
This is the METexon14 skipping variant in the cancer_introns.GRCh38.Jun232020.tsv: chr7:116771655-116774880 MET^ENSG00000105976.13 LUAD:12:2.14,LUSC:2:0.37,LGG:1:0.19 NA METx14del
Do you have any idea why the intron is not categorized in "cancer introns"?
The command I ran: CTAT-SPLICING/STAR_to_cancer_introns.py --SJ_tab_file /input_files/sf_options/205674_sf.SJ.out.tab --chimJ_file /input_files/sf_options/205674_sf.Chimeric.out.junction --vis --bam_file /input_files/sf_options/205674_sf.Aligned.out.sorted.bam --output_prefix 205674_sf --sample_name 205674_sf --ctat_genome_lib /ctat_genome_lib_build_dir
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Chih-Fan
Hi,
I am trying to use ctat-splicing to detect METexon14 skipping but it doesn't seem to work. In the "prefix.introns" file, I do see the variant. However, it does not appear in the "prefix.cancer.introns" file.
This is the record in the ouput "prefix.introns" file:
7:116771655-116774880 + MET^ENSG00000105976 14 0This is the METexon14 skipping variant in the cancer_introns.GRCh38.Jun232020.tsv:
chr7:116771655-116774880 MET^ENSG00000105976.13 LUAD:12:2.14,LUSC:2:0.37,LGG:1:0.19 NA METx14delDo you have any idea why the intron is not categorized in "cancer introns"?
The command I ran:
CTAT-SPLICING/STAR_to_cancer_introns.py --SJ_tab_file /input_files/sf_options/205674_sf.SJ.out.tab --chimJ_file /input_files/sf_options/205674_sf.Chimeric.out.junction --vis --bam_file /input_files/sf_options/205674_sf.Aligned.out.sorted.bam --output_prefix 205674_sf --sample_name 205674_sf --ctat_genome_lib /ctat_genome_lib_build_dir