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Quality check of oxford nanopore sequencing data

I have used pore package in R for read-length histogram from MinION FAST5 files. After using the command read.fast5.info() when i am using the command run.summary.stats(data1) no values are coming in the results. Example result:

                       stat value
1     Templates: Number          0
2     Templates: Max length     0
3     Templates: Min length      Inf
4     Templates: Mean length  NaN
5     Templates: SD length      NA
6     Complements: Number     0
7     Complements: Max length     0
8     Complements: Min length      0
9     Complements: Mean length   0
10   Complements: SD length       0
11           2D failed                         0
12           2D: Number                    0
13           2D: Max length               0
14           2D: Min length                0
15           2D: Mean length             0
16           2D: SD length                 0

For this no plot can be generated to understand the read statistics. can anyone help me with this issue?

r sequencing
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updated by lieven.sterck lieven.sterck • written by MG_19 • MG_19

You may want to try nanoplot and nanoQC from Nanopack.

Edit: fast5 files are not supported by nanopack. You should basecall your data and then use sequencing_summary.txt file to do QC/visualization.

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written by GenoMax GenoMax

I second this suggestion. Nanoplot is what you want.

poRe was released back in 2015ish during MinION early access program, and I don't think Mick or anyone has maintained it since. Sourceforge shows the last changes were made 3 years ago.

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written by kapsakcj kapsakcj

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