Should we label lncRNA as protein_coding feature for cellranger?

[Rohit-Satyam]

I was going through one of the papers that uses CellRanger in Plasmodium and it says(See section Single-cell sequencing and data processing):

Read mapping, deconvolution of cell barcodes and UMIs and the generation of single cell expression matrices were performed using the CellRanger pipeline v 3.0.0. lncRNA regions were labeled as ‘protein coding’ to be prioritized in STAR mapping in CellRanger. CellRanger was also run separately for each sample using the 3D7 reference genome that did not contain the appended non-coding regions for comparison.

Can you explain why lncRNA were tagged as protein coding and if it should always be like this when running cellranger with GTF file containing lncRNA annotation? Does cellranger disconsiders the lncRNA from GTF file?

[github-actions]

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