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WGLab / DeepMod

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications
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where to download albacore v2.3+ #23

Closed Zhenhuiz closed 4 years ago

Zhenhuiz commented 4 years ago

Hi,

I converted multiFast5 into single fast5 with ot_fast5_api. But deepmod still can not recognize my data and said 'no event data'. So I'm thinking re-basecalling with albacore. I searched online, but can't find where to download it. Do you know where I can download it? Thank you!

liuqianhn commented 4 years ago

Hi @Zhenhuiz , yes, fast5 need to be basecalled with events before it is used as input of deepmod. For albacore, you can download from community.nanoporetech.com where you need registration first.

Zhenhuiz commented 4 years ago

Hi @liuqianhn Thank you!

I finally found it! But after re-basecalling, I still got error. 'Error!!! No events data in ./new_basecall/workspace/pass/6/fde91fc4-aa00-4012-9ecb-0fd751c8fc7b.fast5'

Here is the fast5 file:

/ Group /Analyses Group /Analyses/Basecall_1D_000 Group /Analyses/Basecall_1D_000/BaseCalled_template Group /Analyses/Basecall_1D_000/BaseCalled_template/Fastq Dataset {SCALAR} /Analyses/Basecall_1D_000/Summary Group /Analyses/Basecall_1D_000/Summary/basecall_1d_template Group /Analyses/Basecall_1D_001 Group /Analyses/Basecall_1D_001/BaseCalled_template Group /Analyses/Basecall_1D_001/BaseCalled_template/Events Dataset {1208} /Analyses/Basecall_1D_001/BaseCalled_template/Fastq Dataset {SCALAR} /Analyses/Basecall_1D_001/Configuration Group /Analyses/Basecall_1D_001/Configuration/basecall_1d Group /Analyses/Basecall_1D_001/Summary Group /Analyses/Basecall_1D_001/Summary/basecall_1d_template Group /Analyses/Calibration_Strand_Detection_000 Group /Analyses/Calibration_Strand_Detection_000/Configuration Group /Analyses/Calibration_Strand_Detection_000/Configuration/calib_detector Group /Analyses/Calibration_Strand_Detection_000/Summary Group /Analyses/Calibration_Strand_Detection_000/Summary/calibration_strand_template Group /Analyses/Segmentation_000 Group /Analyses/Segmentation_000/Summary Group /Analyses/Segmentation_000/Summary/segmentation Group /Analyses/Segmentation_001 Group /Analyses/Segmentation_001/Configuration Group /Analyses/Segmentation_001/Configuration/event_detection Group /Analyses/Segmentation_001/Configuration/stall_removal Group /Analyses/Segmentation_001/Summary Group /Analyses/Segmentation_001/Summary/segmentation Group /Raw Group /Raw/Reads Group /Raw/Reads/Read_138 Group /Raw/Reads/Read_138/Signal Dataset {9570/Inf} /UniqueGlobalKey Group /UniqueGlobalKey/channel_id Group /UniqueGlobalKey/context_tags Group /UniqueGlobalKey/tracking_id Group

liuqianhn commented 4 years ago

Hi @Zhenhuiz, This is because the events information is not under the default path (Basecall_1D_000). You can use --basecall_1d Basecall_1D_001 (This setting is assumed that events information under Basecall_1D_001 in all fast5 files). If events are under different paths in different files, it would be better to remove old basecall information from fast5 files before re-basecalling.

Zhenhuiz commented 4 years ago

Hi @liuqianhn Could you tell more about where should I use --basecall_1d Basecall_1D_001? In basecalling step or deepmod detect step? And how events information looks? I can only find my fast5 but I don't know where event file is. Thank you!

liuqianhn commented 4 years ago

Hi @Zhenhuiz , --basecall_1d Basecall_1D_001 is a parameter for deepmod. event is in fast5 file. In your fast5 file, if you can see /Analyses/Basecall_1D_001/BaseCalled_template/**Events**, it is basecalled with event.

liuqianhn commented 4 years ago

No further update, and thus I close it. Feel free to re-open it if you need help.