ghuls
commented
6 days ago For the motif to TF table you could take the fly/mouse/human motif to TF tables we provide and match them to kilifish homologs (change the gene_name column with the kilifish homologs).
For your gene regions you can get 10kb upstream and downstream of each TSS (so 20kb regions) and/or another set of 500bp upstream and 100 bp downstream of the TSS for another database (depending on the species you might need to tweak those values a bit e.g 5kb up/down might work better for yours species).
You can use pycistopic tss to get some of the needed files relatively easily:
# Get Ensembl gene annotation name for Killifish.
$ pycistopic tss gene_annotation_list -f killifish
nfurzeri_gene_ensembl Turquoise killifish genes (Nfu_20140520)
$ Get TSS for each gene from Ensembl.
$ pycistopic tss get_tss -n nfurzeri_gene_ensembl -o nfurzeri_gene_ensembl.tss.bed
- Get TSS annotation from Ensembl BioMart with the following settings:
- biomart_name: "nfurzeri_gene_ensembl"
- biomart_host: "http://www.ensembl.org"
- transcript_type: ['protein_coding']
- use_cache: True
- Writing TSS annotation BED file to "nfurzeri_gene_ensembl.tss.bed".
# Sort BED file with TSS.
$ sort -k 1,1 -k2,2n -k3,3n nfurzeri_gene_ensembl.tss.bed > nfurzeri_gene_ensembl.tss.sorted.bed
# Get chromosome name to size mapping.
# For most standard species the following would work, but not for Killifish apparently.
# Get killifish NCBI accession ID.
$ pycistopic tss get_ncbi_acc -s killifish
accession assembly_name
GCF_027789165.1 UI_Nfuz_MZM_1.0
GCF_001465895.1 Nfu_20140520
$ pycistopic tss get_ncbi_chrom_sizes_and_alias_mapping --ncbi GCF_027789165.1 --chrom-sizes-alias nfurzeri.chrom_sizes_and_alias.tsv
Traceback (most recent call last):
File "/home/luna.kuleuven.be/u0079808/software/anaconda3/envs/pycistopic_3.11/bin/pycistopic", line 8, in <module>
sys.exit(main())
^^^^^^
File "/home/luna.kuleuven.be/u0079808/PycharmProjects/pycisTopic/src/pycisTopic/cli/pycistopic.py", line 26, in main
args.func(args)
File "/home/luna.kuleuven.be/u0079808/PycharmProjects/pycisTopic/src/pycisTopic/cli/subcommand/tss.py", line 491, in run_tss_get_ncbi_chrom_sizes_and_alias_mapping
get_chrom_sizes_and_alias_mapping_from_ncbi(
File "/home/luna.kuleuven.be/u0079808/PycharmProjects/pycisTopic/src/pycisTopic/cli/subcommand/tss.py", line 398, in get_chrom_sizes_and_alias_mapping_from_ncbi
ga.get_chrom_sizes_and_alias_mapping_from_ncbi(
File "/home/luna.kuleuven.be/u0079808/PycharmProjects/pycisTopic/src/pycisTopic/gene_annotation.py", line 475, in get_chrom_sizes_and_alias_mapping_from_ncbi
chrom_sizes_and_alias_df_pl = pl.from_dicts(reports).select(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/luna.kuleuven.be/u0079808/software/anaconda3/envs/pycistopic_3.11/lib/python3.11/site-packages/polars/dataframe/frame.py", line 8873, in select
return self.lazy().select(*exprs, **named_exprs).collect(_eager=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/luna.kuleuven.be/u0079808/software/anaconda3/envs/pycistopic_3.11/lib/python3.11/site-packages/polars/lazyframe/frame.py", line 2034, in collect
return wrap_df(ldf.collect(callback))
^^^^^^^^^^^^^^^^^^^^^
polars.exceptions.ColumnNotFoundError: ucsc_style_name
# For Killifish you can use get_chromosome_sizes: https://gist.github.com/andrewyatz/a3687b573364f65904e2
./get_chromosome_sizes.py 'nothobranchius_furzeri' > nothobranchius_furzeri.chrom_sizes.tsv
# Create BED file with regions 20kb up and downstream of TSS.
$ bedtools slop -l 20000 -r 20000 -s -i nfurzeri_gene_ensembl.tss.sorted.bed -g nothobranchius_furzeri.chrom_sizes.tsv > nfurzeri_gene_ensembl.tss.sorted.20kb_up_and_down.bed
# Create BED file with regions 500bp upstream and 100bp downstream of TSS.
$ bedtools slop -l 500 -r 100 -s -i nfurzeri_gene_ensembl.tss.sorted.bed -g nothobranchius_furzeri.chrom_sizes.tsv > nfurzeri_gene_ensembl.tss.sorted.500bp_up_and_100bp_down.bed
juhi-ku
Hello,
I am working on TBI in killifish using bioinformatics approach. I want to investigate killifish clusters and it’s subclusters as it is not very well studied. I want to discover the cell types and clusters and to do so I was planning to work on Gene Regulatory analysis using SCENIC as it has an option to make custom database. Since you and your other colleagues have made the software, I was hoping if you could help me in creating the database for killifish as well. For Killifish we have Ensemble genome (https://www.ensembl.org/Nothobranchius_furzeri/Info/Index ) and Transcription factor list (from the TFDB database) but we do not have any Motif information. Can you let me know if this information is sufficient to proceed? I had a look already into the codes on GitHub, but I still wanted to ask and confirm and seems a bit tough myself to proceed so if you could help me or let me know how it’s done, would be a great help in my research and to the killifish community as well!