🚧 This pipeline is under construction 🚧
Feel free to try to use anything in here, but I make no promises that it will work as it is supposed to.
TransMap is an analysis pipeline for cross-species comparative transcriptome analyses. Building off the framework of SAMap (manuscript; GitHub), TransMap does this by performing Homology-Weighted Transcriptome Expression Mapping to map expression of one species onto another by weighting the expression of similar transcripts via reciprocal BLAST searches.
| Flag | Description |
|---|---|
| -t | Folder containing fastas for each species transcriptome named as Genus_species.fasta [default: transcriptomes] |
| -s | Species tree for creation of homology graph [default: species_tree.newick] |
| -q | Query hsp coverage for BLAST searches [default: 50] |
| -e | Folder containing tab-delimited TPM values for individuals of each species named as Genus_species.txt [default: expression] |
| -m | Tab-delimited file of metadata for each sample with the first column matching the sample names in the expression files. [default: metadata.txt] |
| -c | Number of cpus to speed up some steps. [default: $CPU] |
This page and the corresponding publication are under development. I will update this section with the publication once complete. If you use this pipeline prior its publication, please cite this GitHub repository.