0 motifs loaded

[RadPa]

Hi, I am working on insect data, as suggested by earlier posts, I used createPwm.py to create jaspar_insect. But when I run the motifanalysis-matching does not load motifs (0 motifs). Apart from default jaspar_vertebrate, no other load the motifs. Can you please help, I do not know what's wrong, is my data or the way I am analyzing it. RGT-HINT v0.13.1 python3.7 python3 createPwm.py -i JASPAR2020_CORE_insects_non-redundant_pfms_jaspar.txt -f jaspar-2016 -o jaspar_insect rgt-motifanalysis matching --motif-db jaspar_insect --organism ins --input-files at1.bed an1.bed at2.bed an2.bed

genome: ins pseudocounts: 1.0 fpr threshold: 0.0001

loading input files..

at1, 357224 regions an1, 333812 regions at2, 395054 regions an2, 317038 regions

loading external motif databases..

jaspar_insect

motifs loaded: 0

matching [at1], 357224 regions... [8.620 seconds] matching [an1], 333812 regions... [8.857 seconds] matching [at2], 395054 regions... [10.146 seconds] matching [an2], 317038 regions... [8.291 seconds]

[fabio-t]

Small typo in the arguments, try with --motif-dbs

[RadPa]

I tried --motif-dbs, still, 0 motifs loaded.

[fabio-t]

OK, I'll try to replicate it and get back to you.

[RadPa]

Hi, One of the older posts helped in solving the issue. I changed jaspar_insect to jasper-insect, and it worked. Sorry for the inconvenience. Thank you.

[RadPa]

Except for default jaspar_vertebrate, other databases do not load the motifs. rgt-motifanalysis matching --motif-dbs uniprobe_primary --organism ins --input-files at1.bed an1.bed at2.bed an2.bed

[fabio-t]

Hi @RadPa, the option --motif-dbs is used for the quick & dirty loading of external motif databases, like the one you created. If you don't have a directory called uniprobe_primary where you type that command, it won't work the way you think.

For example, assuming you have a default rgtdata path, try this: --motif-dbs ~/rgtdata/motifs/uniprobe_primary

With reference to jaspar-insect, to be honest, the underscore should not matter at all. So it probably wasn't that the issue.

You should read this page, specifically the section "Hard way": https://www.regulatory-genomics.org/motif-analysis/additional-motif-data/

It will teach you how to setup jaspar insects with metadata, and how to add it to data.config.user to the list of your repositories. You can then use the filter option (read the documentation to see how it works) to use insect or other dbs for specific experiments.

[fabio-t]

Please reopen this if something still not working or clear. Closing for now.

[RadPa]

Thank you for the mail and clarification. I will read the section you have mentioned, and if I reencounter the issue, I will reopen the issue. I apologize for the delayed mail.

Good Day Radhika

On Fri, Apr 2, 2021 at 8:58 PM Fabio Ticconi @.***> wrote:

Hi @RadPa https://github.com/RadPa, the option --motif-dbs is used for the quick & dirty loading of external motif databases, like the one you created. If you don't have a directory called uniprobe_primary where you type that command, it won't work the way you think.

For example, assuming you have a default rgtdata path, try this: --motif-dbs ~/rgtdata/motifs/uniprobe_primary

With reference to jaspar-insect, to be honest, the underscore should not matter at all. So it probably wasn't that the issue.

You should read this page, specifically the section "Hard way": https://www.regulatory-genomics.org/motif-analysis/additional-motif-data/

It will teach you how to setup jaspar insects with metadata, and how to add it to data.config.user to the list of your repositories. You can then use the filter option (read the documentation to see how it works) to use insect or other dbs for specific experiments.

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