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nanoporetech / ont_fast5_api

Oxford Nanopore Technologies fast5 API software
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multi_to_single_fast5 problem #69

Closed FerchoHQ closed 2 years ago

FerchoHQ commented 2 years ago

Hello, I have an issue, when I used multi_to_single_fast5 in order to get a single fast5 file, I find a folder with too many fast5s for each fast5 file that I have; in other words, the program multiplies the number of files by ten times or more. My script:

multi_to_single_fast5 -i /work/yaolab/fernandohq/2021-Dec-assembly_dataset/SRR12801740-ecoli-ontlig \ -s /work/yaolab/fernandohq/2021-Dec-assembly_dataset/SRR12801740-ecoli-ontlig --recursive -t 32

Thanks for your attention.

fbrennen commented 2 years ago

Hi @FerchoHQ -- multi_to_single_fast5 creates single-read fast5 files (an old format that is now deprecated, but that is still used by some legacy software). It sounds like it's performing exactly as expected. If you want to repack your fast5 files then you should use fast5_subset, though you will need to start by producing a list of all the read_ids present in your files for the --read_id_list argument.

FerchoHQ commented 2 years ago

Hi @fbrennen, I´m new in this analyses, and I expected one file, but now I understand the meaning of single fast5s. The program is running now. Thanks for your time and your help.

fbrennen commented 2 years ago

Glad you got it all figured out. =)