Hi,

I have got my first Nanopore sequencing data and the first step was to see if the data is good. Has anyone has any experience with this kind of data and can tell me how to interpret the results. 

The whole report can be downloaded [here][1] (not sure how to post it here). Allin all it looks quite good to me, but what I'm not sure about are the two images attached here. These are the per base QC and sequencing content. It seems that the beginning of the reads is not good, but this can be probably trimmed by removing adapters etc. But Is it really that i need to remove the first 1000 positions? This seems a bit extreme. 

About the sequencing content, I don't know where to begin. This looks consistent with the first image, where the quality is not good, and if removing these positions, it should get better. but is it ok for the two pairs TG and AC to be so much apart like that?

EDIT:

I have done both pycoQC as well as the minionQC run (R). They show similar results. It can be downloaded from [here][2]
a few of the images are also attached.

![Basecalled reads PHRED quality][3]
![Output over experiment time][4]
![Basecalled reads length vs reads PHRED quality][6]
![Channel activity over time][5]

To me it looks as if the run was past its prime after ~50h. There is no real gain of new reads afterwards. As I'm usually work with mRNA-Seq, I'm not sure how to call the PHRED Quality. I can see that the most reads are of Q ~=8 and most of them are short (which is also expected). But all in all can this run be classified as good?

thanks






![per base QC ][7]
![per base Seq content][8]


  [1]: https://datashare.biochem.mpg.de/s/CL7lvs0b1wMSlZj
  [2]:https://datashare.biochem.mpg.de/s/lkhPxr417F4eI6n
  [3]: /media/images/f4b05e56-2eab-41f0-8b11-46dc209b
  [4]: /media/images/cfd343fd-d3ad-41e6-8d8a-6aa6c81c
  [5]: /media/images/5fb9d993-e5b2-411e-94b6-40df8be8
  [6]: /media/images/f880adb8-691a-4a7a-bfdb-7a185cef
  [7]: /media/images/0f7bf463-05c5-467c-8b94-24c6abd4
  [8]: /media/images/84f7f372-dfb1-438a-a42f-0af1e6b0
a few of your reads are very long and those skew and alter the plots.

there is also no binning for the first 10 bases then it is binning into huge bins subsequently, again makes the plot misleading

do not remove the beginning of the reads for QC reasons, that is rarely an advisable course of action.

I would filter the reads to a more manageable length, say 15K and rerun the QC analysis