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YeoLab / skipper

Skip the peaks and expose RNA-binding in CLIP data
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information about intergenic enriched windows #31

Closed VandaLovejoy closed 2 months ago

VandaLovejoy commented 3 months ago

Hi! Thank you so much for this great tool. I'd like to know how it is possible to get information about enriched intergenic regions using Skipper. Thanks! Vanda

augustboyle commented 3 months ago

Hello Vanda,I have not created a list including intergenic reasons but it is possible to supply your own regions. You could add intergenic windows to the PARTITION and FEATURE_ANNOTATIONS output or you could add intergenic annotations to the GFF input and run the commands to create the windows. Either way you would need to specify a new feature type and include it in the ACCESSION_RANKINGS input.If you know there is a lot of binding in intergenic regions and not so much in known transcripts then another option would be to run a GFF of those alone. This would be a natural use case to support but some gene based features would have to be reworked so it hasn’t happened yet!Courtesy of my phoneOn Aug 12, 2024, at 11:55 AM, VandaLovejoy @.***> wrote: Hi! Thank you so much for this great tool. I'd like to know how it is possible to get information about enriched intergenic regions using Skipper. Thanks! Vanda

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VandaLovejoy commented 3 months ago

thank you!!!

De : Evan Boyle @.> Envoyé : lundi 12 août 2024 17:01 À : YeoLab/skipper @.> Cc : Vanda Gaonac'h-Lovejoy @.>; Author @.> Objet : Re: [YeoLab/skipper] information about intergenic enriched windows (Issue #31)

Hello Vanda,I have not created a list including intergenic reasons but it is possible to supply your own regions. You could add intergenic windows to the PARTITION and FEATURE_ANNOTATIONS output or you could add intergenic annotations to the GFF input and run the commands to create the windows. Either way you would need to specify a new feature type and include it in the ACCESSION_RANKINGS input.If you know there is a lot of binding in intergenic regions and not so much in known transcripts then another option would be to run a GFF of those alone. This would be a natural use case to support but some gene based features would have to be reworked so it hasn’t happened yet!Courtesy of my phoneOn Aug 12, 2024, at 11:55 AM, VandaLovejoy @.***> wrote: Hi! Thank you so much for this great tool. I'd like to know how it is possible to get information about enriched intergenic regions using Skipper. Thanks! Vanda

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: @.***>

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