Data for SAMap comparison of S. canicula developing telencephalon to mouse and salamander

This is the data created/contained in the project folder for the SAMap comparison of S. canicula developing telencephalon to mouse and salamander.

raw/ contains the raw data for each species. This entails the fully annotated single-cell object in .RDS format, its conversion to .h5ad format, the GFF annotation file of the genome version used in the project, EggNOG-mapper annotations for the proteome, the proteome FASTA file, and a table that maps gene IDs to protein IDs.

processed/ contains the results of pre-processing the data (see "prepare" section of the SAMap code repository). Per species, this is a .h5ad file that contains counts and metadata, as well as the peptide FASTA.

aln/ contains the pairwise all-against-all alignments between S. canicula and the other species, as produced by MMseqs2, in the m8/ folder. The mmusscan/ and pwalscan/ folders contain the pairwise alignments of the respective species in the format expected by SAMap. Finally, the log files of the alignments are also included.

results/ contains the results of the analysis. These are the pickled pairwise SAMap comparison objects (scan_mmus.pkl and scan_pwal.pkl), the collated SAMap similarity matrix (collated.csv) and various plots generated during the comparison. For details, please refer to the Jupyter notebook of the analysis.