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AlexsLemonade / alsf-scpca

Management and analysis tools for ALSF Single-cell Pediatric Cancer Atlas data.
BSD 3-Clause "New" or "Revised" License
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Adjust reference scripts to make files needed for splici index #95

Closed allyhawkins closed 3 years ago

allyhawkins commented 3 years ago

Related to adding additional samples in #92 to be analyzed in alevin-fry using the splici index with the USA mode. I thought this would be an easy fix of just adding a few lines to generate the 3 column version of the tx2gene.tsv needed to run alevin-fry in USA mode. However, the steps outlined in the alevin tutorial are a bit different with some additional steps that we had not had prior to this. This results in a different splici.fasta, that is not exactly the same as the spliced_intron.fasta we originally were generating. We will need to add the necessary steps to generate these files to our current make_pre_mrna_fasta.R before processing any samples using the splici index.

allyhawkins commented 3 years ago

The splici index has now been updated according to the alevin tutorial and is located in s3 here for alevin-fry: s3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-103/salmon_index/spliced_intron_txome_k31