Do we need to run "ctat-LR-fusion --prep_reference" once for each sample?

[Luobin Yang]

Hi, 

The documentation says we only need to run once to prepare the reference genome, but the command also takes a -T fastq file with "--prep_reference" option. I am wondering how does the fastq input file affect the output minimpa2 index?

Thanks,
Luobin

[Brian Haas]

Hi Luobin,

After the reference is built, you can just run ctat-LR-fusion with just the -T option (no need for --prep_reference).  If you do include the option and the reference is built, I expect it should just ignore it and not try to rebuild it again.

The -T input has no effect on the genome index.

best,

Brian

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

 

[Luobin Yang]

Hi Brian, thanks for the clarification!