Advanced use cases

SCALT is quite versative since it allows to mix the different utilities depending on the needs of the user. The following instructions refer to advanced strategies which go behyond classifying cells or generate cell type specific list of genes.

Use custom lists in SCALT.py

Suppose that the pipeline of SCALT_AnnotaionListsBuilder.py was exploit to generate the cell type specific lists of genes from an annotation file. The idea is to use these lists for classification. Therefore, the directory containg the lists of SCALT.py must be changed.

This can be achieved adjusting a parameter of the classifier in this way:

python3 SCALT.py new_read_counts.tsv -Types custom -Notation gene_symbol -Min 300 -CPUs 2

Or

python3 SCALT.py new_read_counts.tsv --Types custom --Notation gene_symbol --Threshold 300 --CPUs 2

Changing the paratemeter value of Types to custom forces SCALT.py to use the lists of genes originated from the annotation file as reference lists for classification.

Use naive lists in SCALT.py

In the case in which the pipeline of SCALT_NaiveListsBuilder.py was utilized to generate the cell type specific lists of genes and the user wants to use these lists for classification, the directory of SCALT.py must be updated.

This can be done adjusting a parameter of the classifier in this way:

python3 SCALT.py new_read_counts.tsv -Types naive -Notation gene_symbol -Min 300 -CPUs 2

Or

python3 SCALT.py new_read_counts.tsv --Types naive --Notation gene_symbol --Threshold 300 --CPUs 2

Changing the paratemter value of Types to naive forces SCALT.py to use the lists of genes originated from the user-defined lists as reference for classification.

Note

It is important that, in both previously described cases, the new counts used in the classification must have the same gene notation of the counts used for the generation of the lists. So, if the gene symbols are present, specify -Notation gene_symbol or –Notation gene_symbol. Differently, if the ensembl ids are used, specify -Notation ensembl_id or –Notation ensembl_id or leave default setting.