[QUERY] Can I test UNCALLED to always try and map only 2000 raw samples from FAST5

skovaka / UNCALLED

Raw nanopore signal mapper that enables real-time targeted sequencing

MIT License

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[QUERY] Can I test UNCALLED to always try and map only 2000 raw samples from FAST5 #40

Open harisankarsadasivan opened 2 years ago

harisankarsadasivan commented 2 years ago

@skovaka However long a read maybe, I want to always test UNCALLED by letting it map only 2000 samples from a read, offline. How may I achieve this? Is changing the for loop limits here sufficient or do I need to do more? Would adapter trimming be taken care of?

skovaka commented 2 years ago

I just added options to adjust the chunk size and time in uncalled map. Try running with the options --chunk-time 0.5 --max-chunks 1, which will set the maximum number of samples to 4000*0.5*1 = 2000. You'll have to pull the latest version and reinstall to see those options. UNCALLED doesn't do any adapter trimming, so that won't be affected. Hope that helps!