no decent genome annotation, how to run the software?

[joleneyue]

Dear Nadia,

i would like to ask you one more question considering what i want to achieve in my analysis using your software.

i do not have a very decent genome annotation, but i want to use the stringtie.gtf to merge with the trinity.fasta which are all generated myself individually into the necklace without filtering with the related species.( i assume this step is done in blat or lace)

more details, 1 .i do not want to use the genome annotation .gtf file because i do not have a proper one( my genome is not perfect and not published yet). can i feed the stringtie.gtf file to the genome annotation instead? it seems that if i do not give a file there, it does not run properly.

2. i do not want to use the related species to filter out the genes , which do not exist in the related species genome.

Please let me know if i can achieve this idea by this software or anything i can adjust. Thanks a lot for your help and time!!

Cheers, Yuling

[nadiadavidson]

Hi Yuling,

For 1. You could pass the stringtie.gtf file as the reference annotation if you want to and that should make the pipeline run. However, I think you could also safely give the reference annotation even if it is bad. The idea of Necklace is to add all the information together, so the reference annotation shouldn't take away from the stringties assembly. For 2. Only de novo assembled genes which are not found in a related species OR the reference annotation OR stringties assemblies get filtered out. So these are sequences which do not align to the genome or look like known coding sequence. Genes which are in your reference annotation or stringties gtf won't be filtered out, even if they aren't seen in the related species. This is just a way to clean up the de novo assembly and can't really be switched off easily in the pipeline.

Hope some of that information is useful.

Cheers, Nadia.

[joleneyue]

Thanks you very much for your kind reply.

Cheers, Yuling

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From: nadiadavidson @.> Sent: Thursday, March 17, 2022 12:20:24 AM To: Oshlack/necklace @.> Cc: Yuling Yue @.>; Author @.> Subject: Re: [Oshlack/necklace] no decent genome annotation, how to run the software? (Issue #18)

Hi Yuling,

For 1. You could pass the stringtie.gtf file as the reference annotation if you want to and that should make the pipeline run. However, I think you could also safely give the reference annotation even if it is bad. The idea of Necklace is to add all the information together, so the reference annotation shouldn't take away from the stringties assembly. For 2. Only de novo assembled genes which are not found in a related species OR the reference annotation OR stringties assemblies get filtered out. So these are sequences which do not align to the genome or look like known coding sequence. Genes which are in your reference annotation or stringties gtf won't be filtered out, even if they aren't seen in the related species. This is just a way to clean up the de novo assembly and can't really be switched off easily in the pipeline.

Hope some of that information is useful.

Cheers, Nadia.

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