Inv output question

[GLagunas-Robles]

Hello!

Thanks for this awesome program!

Is there a way to "choose" the standard orientation for the inv.png output. For example, I made this toy example, where the first sequence is the standard arrangment, the following sequence is an inverted arrangement, and the third is a segment of std, inv, std, inv that is aligning correctly.

[AndreaGuarracino]

You can try odgi flip. It has the --ref-flips option to flip paths to match the orientation of the specified path(s).

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________________________________ From: German Lagunas-Robles ***@***.***> Sent: Wednesday, December 18, 2024 14:09 To: pangenome/pggb ***@***.***> Cc: Subscribed ***@***.***> Subject: [pangenome/pggb] Inv output question (Issue #434) Hello! Thanks for this awesome program! Is there a way to "choose" the standard oreintation for the inv.png output. For example, I made this toy example, where the first sequence is the standard arrangment, the following sequence is an inverted arrangement, and the third is a segment of std, inv, std, inv that is aligning correctly. image.png (view on web)<https://github.com/user-attachments/assets/db2b269f-9890-4d0d-ab9e-747eb3f29d16> — Reply to this email directly, view it on GitHub<#434>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AO26XHUAYPIYLC35KNRX3M32GHJBPAVCNFSM6AAAAABT3O5JJ6VHI2DSMVQWIX3LMV43ASLTON2WKOZSG42DQNRWGQ3DCOI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[GLagunas-Robles]

Thanks for your quick response!

Hmm... so the three paths from top to bottom are the standard path, the inverted path, and a combination of standard+inverted path. I tried different combinations of --ref-flips and --no-flips, but the path that is peculiar is the standard path that is initially painted red with the default run.

Here is the standard path declared as --no-flips, but it reverses the inverted path and now calls both inverted path and the standard path as reverse. When I declare the standard path for --ref-flips, it results in the same graph below.

The 25kb toy inversion that is being difficult is std, inv, std, inv variant of the standard path. I declared a segment length of 2k on my initial pggb run (the previous two graphs) because if I went above 10k it would call the third path as a combination of of standard plus unique sequence when it is simply a rearrangement of the standard path (attached below).

Here are my settings for the pggb run. Any suggestions for setting up the run and choosing optimal parameters would be greatly appreciated!

2k run

-n 3 -p 90 -s 2k -k 79

10k run

-n 3 -p 90 -s 10k -k 79