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valenlab / amplican

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Sample size issue #19

Open yingxins opened 4 months ago

yingxins commented 4 months ago

Hello, when I run Amplican on my own files, I have this error: Error: 'sampsize' = 1000 should not be larger than the number of objects, 305

However, our sample size is 19, neither 305 or 1000.

Can you help me figure out where it goes wrong?

Here is my code:

`path <- getwd() config <- paste0(path,"/F3MVRM_results/copy.csv") fastq_folder <- paste0(path,"/F3MVRM_results/F3MVRM_raw") results_folder <- paste0(path, "/F3MVRM_results/amplican_result")

parameter explanation fastqfiles

amplicanPipeline(config, fastq_folder, results_folder,fastqfiles = 1)`

Here is myconfig file:

trialconfig.csv

JokingHero commented 4 months ago

Can you paste whole error instead of last line only?

Also, I recommend to use one uppercase segment inside the amplicon column in your config files. Normally its guide region. When you have more than one then it is using the most left upper region as the region where you expect the cuts.

Additionally, you could try to run the pipeline with option event_filter = FALSE