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SchulzLab / SNEEP

SNp Exploration and Analysis using EPigenomics data
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How to run sneep on a non-model organism? #9

Open BaumgartenNina opened 5 months ago

BaumgartenNina commented 5 months ago

Following up on your previous question @biouserPD

To run sneep you need:

If these information are available one needs to recompute the scale parameters for the new set of PWMs, which I also can explain to you in detail.

Do you have the sequence and a set of PWMs of interest?

regards Nina

biouserPD commented 5 months ago

Hi Nina, I have the genome in fasta format but I'm not very sure if there are the TF binding motifs specific for sea bass in the Jaspar database, which is the species I'm studying. I will do more in-depth research. Thank you very much for helping Best, Max

Il giorno lun 25 mar 2024 alle ore 12:07 BaumgartenNina < @.***> ha scritto:

Following up on your previous question @biouserPD https://github.com/biouserPD

To run sneep you need:

  • the genome of your favourite organism in fast format
  • a list of species specific TF binding motifs (PWMs) in TRANSFAC format (for instance downloaded from the JASPAR database)

If these information are available one needs to recompute the scale parameters for the new set of PWMs, which I also can explain to you in detail.

Do you have the sequence and a set of PWMs of interest?

regards Nina

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SchulzLab commented 5 months ago

I suggest to take either vertebrate matrices from Jaspar or matrices from the evolutionary closed fish species that is listed in Jaspar.

biouserPD commented 4 months ago

Hi, I downloaded the vertebrate matrix in transfac format from the jaspar database. Now I should estimate a new scale parameter b for a non human species. Is there a script or special command to do that? Thanks again for your help, Max

Il giorno lun 25 mar 2024 alle ore 15:21 SchulzLab @.***> ha scritto:

I suggest to take either vertebrate matrices from Jaspar or matrices from the evolutionary closed fish species that is listed in Jaspar.

— Reply to this email directly, view it on GitHub https://github.com/SchulzLab/SNEEP/issues/9#issuecomment-2018116540, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVMHEP4JODXHWJJY6BAKMDY2AXGJAVCNFSM6AAAAABFGZPKOKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJYGEYTMNJUGA . You are receiving this because you were mentioned.Message ID: @.***>

-- Massimiliano Babbucci, PhD Department of Comparative Biomedicine and Food Science (BCA) University of Padova Viale dell'Universita' 16, Agripolis I-35020 Legnaro (PD), Italy ORCID: https://orcid.org/0000-0002-4060-4728 Tel: + 39 049 8272506 e-mail: @.***

BaumgartenNina commented 4 months ago

Hi,

yes, there is a script to do so. We are currently working on adding this part to the documentation. I will let you know once we updated it.

Best, Nina

biouserPD commented 3 months ago

Hi, I noticed that in the result.txt file the last field instead of being the "fdr_corrected_pvalue" still contains the strand information (always the word forward). Here an example of my result.txt: chr7:23877410-23877411 T C chr7_23877411 -1 .::chr7:23877360-23877461 GFI1 chr7:23877406-23877418 (f) 5 0.000078 0.001851 -3.161762 8.303852e-03 forward chr7:23877410-23877411 T C chr7_23877411 -1 .::chr7:23877360-23877461 TFCP2 chr7:23877407-23877417 (f) 4 0.029778 0.001428 3.037724 6.598875e-03 forward chr7:23877410-23877411 T C chr7_23877411 -1 .::chr7:23877360-23877461 GRHL1 chr7:23877406-23877417 (f) 5 0.009861 0.000467 3.050853 5.710945e-03 forward chr7:23877410-23877411 T C chr7_23877411 -1 .::chr7:23877360-23877461 GRHL2 chr7:23877407-23877417 (r) 7 0.001626 0.000051 3.471028 4.114462e-03 forward

Best, Max

Il giorno ven 19 apr 2024 alle ore 08:53 BaumgartenNina < @.***> ha scritto:

Hi,

yes, there is a script to do so. We are currently working on adding this part to the documentation. I will let you know once we updated it.

Best, Nina

— Reply to this email directly, view it on GitHub https://github.com/SchulzLab/SNEEP/issues/9#issuecomment-2065874605, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVMHEKWGT4SEBFULT55BPTY6C5NFAVCNFSM6AAAAABFGZPKOKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRVHA3TINRQGU . You are receiving this because you were mentioned.Message ID: @.***>

-- Massimiliano Babbucci, PhD Department of Comparative Biomedicine and Food Science (BCA) University of Padova Viale dell'Universita' 16, Agripolis I-35020 Legnaro (PD), Italy ORCID: https://orcid.org/0000-0002-4060-4728 Tel: + 39 049 8272506 e-mail: @.***