GRCh38_gencode_v44 vs v45

[Asher Preska Steinberg]

Hi there,

Thank you for building all of these wonderful resources. I have a couple questions about the kickstart mode of ctat-lr-fusion described here. 

1) My ONT RNAseq data is aligned with minimap2 to the primary assembly of Gencode v45 . Is it okay to use the kickstart mode with the plug-n-play reference for GRCh38_gencode_v44 here or should I build a new reference for v45?

2) If I have supplemental illumina RNAseq data, can I use this in kickstart mode along with the ONT bams?

Thanks,

Asher

[Brian Haas]

Hi Asher,

As long as the reads were aligned with minimap2 against the GRCh38 genome, should be fine to try the kickstart mode. Should be fine with ONT bams too.

best,

Brian

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Asher Preska Steinberg]

Great, thank you for your help Brian!

Best,

Asher

[Asher Preska Steinberg]

Hi Brian,

Great, thank you!

Asher