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bioinfomaticsCSU / deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads
GNU General Public License v3.0
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Albacore paramter used for basecalling #54

Closed akk01 closed 4 years ago

akk01 commented 4 years ago

Hi,

For my practice, I downloaded two human Fast5: (1) NA12878.native.simpson.101515 (2) NA12878.native.simpson.103015 from https://www.ebi.ac.uk/ena/browser/view/PRJEB13021. These data were processed with DeepSignal in your paper.

The very first step of DeepSingal is to perform basecalling with Albacore. I performed basecalling with Albacore v2.3.4, which didn't generate any fastq.

Do you know the Albacore parameters such as --flowcell and --kit that you used. I may have been using wrong Albacoere version and paramters.

PengNi commented 4 years ago

Hi @akk01 ,

The NA12878.native.simpson.101515 and NA12878.native.simpson.103015 is sequenced by R7 2D tech, which has been deprecated by ONT. I suggest that you use NA12878/HX1 R9.4 reads (#44 , NA12878, #42 , HX1) for practice.

Best, Peng

akk01 commented 4 years ago

Very helpful. Thanks for the clarification.