Multiple Sample for bPTR

[santoshe1]

Hi Team,

I am running bPTR prediction for multiple samples (30+ samples). I would like to know if there any ways to fasten the process for the bPTR prediction for multiple sam files and multiple genomes.

Command i use:
bPTR -f sample_data/Multiple*(3000Genomes).fna -s sample_data/Multiple(30+Samples)*sam -o test.bPTR.tsv -plot test.bPTR.pdf -m coverage

Kindly assist.

Thanks

[christophertbrown]

Hi, The bottleneck in the process is the time that it takes to read though the SAM files. To speed things up you can parallelize by running several jobs at the same time, each set to a different SAM file (at least until you run into IO issues). For each of those jobs, you should still include paths to the full set of genomes. Hope this helps. Let me know if you have questions. Best, Chris

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On Mar 4, 2019, at 7:51 PM, santoshe1 ***@***.***> wrote: Hi Team, I am running bPTR prediction for multiple samples (30+ samples). I would like to know if there any ways to fasten the process for the bPTR prediction for multiple sam files and multiple genomes. Command i use: bPTR -f sample_data/Multiple*(3000Genomes).fna -s sample_data/Multiple(30+Samples)*sam -o test.bPTR.tsv -plot test.bPTR.pdf -m coverage Kindly assist. Thanks — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.