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How to add motifs in cellranger-arc reference?

Hello,

I am trying to build a reference using cellranger-arc mkref. I would like to include the file with the motifs in the reference from step 3 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/advanced/references#mkref) however I am not sure which file to use. I am using the fasta and gtf files from this link: https://useast.ensembl.org/Danio_rerio/Info/Index

When I search here (https://jaspar.elixir.no/) for zebrafish or Danio rerio I dont find the file that I need. I also looked here but I am not sure which file to use https://jaspar.elixir.no/download/data/2024/CORE/.

Does anyone know which would be the correct file?

Thank you

gtf scrnaseq fasta cellranger
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updated by Ehsan • Ehsan • written by bioinfo • bioinfo

Hi. Do you have any updates on what you ended up doing? I am encountering same issue, cannot really find a good TF motif database for zebrafish. Would appreciate hearing your experience!

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written by Ehsan • Ehsan

1 answer

That'd be because JASPAR has no PWMs derived specifically from zebrafish data. You can search for other PWM databases that contain such info for zebrafish. Or just use the vertebrate core from JASPAR with the understanding that the homology may differ significantly in zebrafish.

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written by jared.andrews07 jared.andrews07

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