problem for fusioncatcher-build

[LEIyuechen]

Hi,

I am trying to use fusioncatcher-build and I need the genome and database of hg37 version. However, the default and "https://sourceforge.net/projects/fusioncatcher/files/data/" is all for hg38. Could I build my hg37 version directory and how I change the parameter?? I tried to go through the code and change the "-e" parameter but it doesn't work. Please show me how to deal it or what should I download by myself.

Hope your reply. Thank you.

Best, Lei

[ndaniel]

Sorry that is not possible. FusionCatcher gives the genomic coordinates of fusion genes in hg38 and hg19 though.

[LEIyuechen]

If I want to build hg19 version genome, What parameter should I use in terms of fusioncatcher-build.py？I cannot find appropriate way to tell programme I want hg19.------------------ 原始邮件 ------------------ 发件人: "Daniel Nicorici"notifications@github.com 发送时间: 2019年7月2日(星期二) 晚上6:58 收件人: "ndaniel/fusioncatcher"fusioncatcher@noreply.github.com; 抄送: "LEIyuechen"747166943@qq.com;"Author"author@noreply.github.com; 主题: Re: [ndaniel/fusioncatcher] problem for fusioncatcher-build (#125)

Sorry that is not possible. FusionCatcher gives the genomic coordinates of fusion genes in hg38 and hg19 though.

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[ndaniel]

FusionCatcher gives the genomic coordinates of fusion in hg38 and hg19 always. The file that file that has hg19 contains the coordinates using hg19. There is no need to build anything because FusionCatcher converts hg38 to hg19.

[Coaxecva]

Hi Ndaniel,

I ran fusioncatcher using human_v102 (from the download script). In the output folder, I couldn't find hg19. Wonder if I missed something in the run?

Thanks, Coax

#Output folder

final-list_candidate-fusion-genes.caption.md.txt
final-list_candidate-fusion-genes.vcf
fusioncatcher.log.002.bak
summary_candidate_fusions.txt
supporting-reads_gene-fusions_STAR.zip final-list_candidate-fusion-genes_sequences.txt.zip
fusioncatcher.log
info.txt
supporting-reads_gene-fusions_BLAT.zip
viruses_bacteria_phages.txt final-list_candidate-fusion-genes.txt
fusioncatcher.log.001.bak
junk-chimeras.txt
supporting-reads_gene-fusions_BOWTIE.zip

[Coaxecva]

Looks like it has only hg38:

source=fusioncatcher_v1.33

reference=ftp://ftp.ensembl.org/pub/release-102/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa

assembly=ftp://ftp.ensembl.org/pub/release-102/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa

phasing=none

geneAnnotation=ensembl_v102

[rpauly]

Did anyone find a solution this problem? I am looking for the hg19 build as well. Thanks!

[Coaxecva]

Hi @rpauly,

I think you just have to run FusionCatcher with hg38. In the result folder, you will find final-list_candidate-fusion-genes.hg19.txt that was converted from hg38.

Previously, I put the option --skip-conversion-grch37 True so there wasn't hg19.

Coax