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PengNi / plant_5mC_analysis

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Question about the coverage calculation. #2

Closed Musketeer-D closed 3 years ago

Musketeer-D commented 3 years ago

Dear Ni, Can you tell me how do you calculate the 'coverage' mentioned in your paper https://doi.org/10.1101/2021.02.07.430077? As you mentioned in #1 , 'at least 20x coverage of reads are needed to get a stable result', do you mean the total read (including fail reads of guppy) or just pass read of guppy should be at least 20x coverage ?

PengNi commented 3 years ago

@musketeerD , thanks for your interest of our tool. We only count reads in PASS directory after basecalling using Guppy. We use samtools to estimate depth of the reads aligned to the reference genome.

Musketeer-D commented 3 years ago

Thank you for your kind help! So,'at least 20x coverage of reads are needed to get a stable result' means I need to have at least 20x mapped pass reads ?

PengNi commented 3 years ago

Yes.

Musketeer-D commented 3 years ago

Thanks so much again!