search

christophertbrown / iRep

scripts for estimating bacteria replication rates based on population genome copy number variation
MIT License
68 stars 9 forks source link

Multiple Sample for bPTR #29

Open santoshe1 opened 5 years ago

santoshe1 commented 5 years ago

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 commented 5 years ago

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

On Mar 4, 2019, at 7:51 PM, santoshe1 notifications@github.com 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.