Transcriptome File Type

[aem11309]

I am attempting to work through your processing examples using my own data sets, and I do not recognize your transcriptome length file type in the run construct_batch pre-processing step (gg_200524_mouse_genome_polyA_cum_1 in your example).

Any assistance on how to generate this file type would be greatly appreciated.

[gennadygorin]

The file type is just a space-separated list in format [name, length, # polyA of length > 4, # polyA of length > 5, ...]. The notebooks used to make these are here:
https://github.com/pachterlab/GP_2021_3/tree/master/processing_scripts/make_references

The raw FASTA files can be obtained from Ensembl BioMart by querying gene name, gene start, and gene end properties for Attributes -> Sequences -> Unspliced (Gene).