problem when loading gff

[Luigi Faino]

Dear Developer

I have an issue when I load the annotation in the annotation track. As you can see, if i load the track as JBrowse track, i can see the correct transcript start while when i load the same gff in the editable track, the start is not the same. Any idea why or how i can fix the problem?

cheers

Luigi

[Colin]

Apollo recalculates what it believes the longest open reading frame is on import I believe, so it does not always preserve what the user imported.

To disable this I believe you can use the setting use_cds_for_new_transcripts documented here https://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=cds 

use_cds_for_new_transcripts=false

Alternatively you can keep the default behavior but just inspect to see if this particular transcript had something weird about it's start site or splicing site

-Colin

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[Colin]

Sorry it might actually be

use_cds_for_new_transcripts=true

For your desired purposes, the default is false

-Colin

[Nathan Dunn]

If you are using the python (https://pypi.org/project/apollo/) library (not sure how you are doing the load), there is a —disable_cds_recalculation option that does the same thing. 

They are equivalent, so I would just continue to use what you were already using.

Nathan

On Sep 6, 2021, at 10:51 AM, Colin <colin...@gmail.com> wrote:

Sorry it might actually be

use_cds_for_new_transcripts=true

For your desired purposes, the default is false

-Colin

On Mon, Sep 6, 2021 at 1:50 PM Colin <colin...@gmail.com> wrote:

Apollo recalculates what it believes the longest open reading frame is on import I believe, so it does not always preserve what the user imported.

To disable this I believe you can use the setting use_cds_for_new_transcripts documented here https://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=cds 

use_cds_for_new_transcripts=false

Alternatively you can keep the default behavior but just inspect to see if this particular transcript had something weird about it's start site or splicing site

-Colin

On Mon, Sep 6, 2021 at 4:59 AM 'Luigi Faino' via apollo <apo...@lbl.gov> wrote:

Dear Developer

I have an issue when I load the annotation in the annotation track. As you can see, if i load the track as JBrowse track, i can see the correct transcript start while when i load the same gff in the editable track, the start is not the same. Any idea why or how i can fix the problem?

cheers

Luigi

<Screenshot from 2021-09-06 10-56-24.png>

________________________________________________________

Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer.
The information contained in this e mail message is strictly confidential and intended for the use of the addressee only.  If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system.

---

Fai crescere i nostri giovani ricercatori
dona il 5 per mille alla Sapienza

codice fiscale 80209930587

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To unsubscribe from this group and stop receiving emails from it, send an email to apollo+un...@lbl.gov.