RPK Export Option

Bug Reports
1

Hi Daniel

Thanks for adding the RPK normalization function. I just gave it a try and have two issues

  1. Using a single meganized DAA file, when I export using the “SEED Path to RPK” option, I always get “0 lines written”, however exporting using “SEED Name to RPK” works fine. “SEED Path to Counts” also works fine

  2. When using the “Compare” option, to view multiple samples simultaneously, I cannot locate the RPK option under the Export CSV sub-menu. This option would be most helpful

Best,
Aditya

2

I’m away for a week but will then fix these issues
D

3

Hi Daniel

Thanks for the update. I gave the latest version (v6.7.1) a try, but I still cant see an RPK export option, when I parse multiple meganized DAA files using the COMPARE option.

The RPK export option seems to work fine for single files. Requesting if this export option can be included when using the COMPARE option

Best,
Aditya

4

Because comparison files do not contain reads and alignments, the export that you are requesting is not easy to implement. However, a comparison files does contain the location of the originally imported files, so, if they are still present, then in theory it would be possible for MEGAN to export what you desire. However, there is a quite a bit of programming overhead, so I need to find time to sit down and implement this… I will try to do so very soon
D

5

Hi Daniel

When I use the export CSV > SEED Path to RPK option, the GUI just freezes, saying its processing the command. Its been running for a few hours now (RAM available is 25G). Is this normal?

Regards,
Aditya

6

Unfortunately, this output requires a lot of I/O and computation, and so it takes a very long time. I will look into speeding this up.