Open JAYRJPT opened 3 years ago
Hi Jay, thanks for trying Clinker!
That error comes during the first stage (generate_fst) where the superTranscripts cannot be located in the reference files given the inputted coordinates.
I noticed hg19 has a IGH@ gene, but not hg38 (at least in Clinker's reference). Did the fusion caller us hg19? If so, simply delete the current output and change your -p genome=38 to -p genome=19.
If you're sure it's hg38, then I'll have to look into why that is missing.
Cheers, Breon.
Hi Breon, I have used Fusioncatcher and it has used hg38 as reference genome. I have mentioned the coordinates of the gene according to hg38 only.
Thanks, Jay
Hi Jay,
Sorry for the delay. I will need to rebuild the references to account for IGH@ in hg38 - it seems Clinker currently doesn't have a superTranscript for that. The bad news is that it might take me some time to get together as I am currently finishing some other projects.
However, I'm a bit confused as to why RABL2B is coming up as the closest gene (chr22), when DUX4 and IGH@ are on other chromosomes in the hg38 reference? Would you mind sharing the csv with the coordinates in them? Otherwise, just double check the positions are accurate.
Thanks! Breon.
Hello I am using Clinker to visualize one of the fusions came from fusion catcher tool. I have made a csv file with the coordinates of the fusion named DUX4:IGH@ similar to the bcr_abl1.csv file mentioned in test folder. Here is my command-
bpipe -p out=/home/deepak/output -p caller=$CLINKERDIR/test/caller/dux4_igh.csv -p col=1,2,3,4 -p genome=38 -p print=true -p competitive=true -p header=true -p align_mem=31025992405 -p genome_mem=31025992405 -p threads=30 -p fusions=DUX4:IGH@ $CLINKERDIR/workflow/clinker.pipe $CLINKERDIR/test/fastq/*.fastq.gz
But I am getting the error at the alignment step
Here is the bpipe error
Any suggestion to remove this error?
Thanks and Regards,
Jay