Is it possible to run sqm_annot.pl with external databases?

[PuspenduSardar]

Hello!

I was wondering if there is a workaround to include external databases while using the sqm_annot.pl script for the functional annotation. Please note that full SqueezeMeta.pl is not possible, and therefore I can't use add_database.pl either to add the external databases later on.

Any suggestion would be very helpful!

Regards, PS

[jtamames]

Hello Not actually. But it would be rather easy to implement. I will look into it. Best, J

[PuspenduSardar]

@jtamames, thank you very much. Please let me know.

Regards, PS

[PuspenduSardar]

Hi @jtamames I was wondering if there are any updates on this issue? Many thanks!

Regards, Puspendu

[jtamames]

Hello I couldn't work on this yet, but it is in my agenda. Thanks for remind me Best, J

[jtamames]

Ok, try this one. Uncompress it and replace your original sqm_annot.pl with this one (rename the original one for not overwriting it in case this one is not working). Specify your external database as it is described in the manual for SqueezeMeta sqm_annot.pl.gz

[PuspenduSardar]

Thanks a lot, @jtamames

I'll give it a try and let you know soon. Just a quick question, if I remove --nopfam from the script, would the PFAM db be used for the annotation? Thank you once again!

Regards, PS

[jtamames]

No, it will be done. Best, J

[fpusan]

Closing due to lack of activity, feel free to reopen!