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aertslab / create_cisTarget_databases

Create cisTarget databases
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FASTA Input to Generate SCENIC+ Databases for Rat #41

Open jonhsussman opened 10 months ago

jonhsussman commented 10 months ago

Hello,

Thanks for the helpful tutorial. I am trying to generate the relevant database files to use SCENIC+ for rat genome. I've generated the motifs table by using the motifs-v10-nr.mgi-m0.00001-o0.0.tbl file and replacing the gene_name with the homologous gene for rat. But it is a little unclear what to use as the other input files for create_cistarget_motif_databases.py. For the motif IDs I am using all the motifs available under "singletons." But I am not sure what is the most correct to use for the fasta filename. Currently, I am trying this with the whole genome (Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa) but it seems that it would make sense for these regions to be filtered in some way.

Is there an example of what was used to generate the databases for mouse/human or other species?

Thanks, Jonathan

ghuls commented 10 months ago

You can use a BED file with pseudobulk peaks from your scATAC data and use bedtools to make the FASTA file:

bedtools getfasta \
    -fi Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa \
    -bed pseudobulk_peaks_from_scATAC.bed \
    -fo rattus_norvegicus.pseudobulk_peaks.fa
jonhsussman commented 10 months ago

Thanks for this explanation, this is very helpful!

On Wed, Aug 16, 2023 at 6:54 AM Gert Hulselmans @.***> wrote:

You can use a BED file with pseudobulk peaks from your scATAC data and use bedtools to make the FASTA file:

bedtools getfasta \ -fi Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa \ -bed pseudobulk_peaks_from_scATAC.bed \ -fo rattus_norvegicus.pseudobulk_peaks.fa

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