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Guppy output move matrix mapping #11

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haotianteng opened this issue Feb 5, 2022 · 0 comments
Open

Guppy output move matrix mapping #11

haotianteng opened this issue Feb 5, 2022 · 0 comments

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@haotianteng
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I was using guppy basecaller Version 5.0.11+2b6dbffa5, and trying to remap the basecalled sequence to the reference, I can roughly get a mapping with the Move matrix provided by Guppy, but I found that the length provided by the move matrix is not the exact same as the signal length.

For example this read, the move matrix has a length L_M 6965
image
And the signal length has a length L_S 76153
image
I was using the rna_r9.4.1_70bps_hac.cfg, according to the document, the stride is 10.
I was expecting the L_S = 10 * L_M, however, this is not the case here as 76153 / 6965 ~ 10.9

So I think guppy may chopping the adapter and polyA tail here, so does that mean the move matrix is aligned with the signal at the tail.

Where I may find this information in the fast5 file?

Thanks

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