working with gene panels or single genes (e.g., NF1) in the nf-core/rnaseq pipeline

[huma1995]

Are there any recommendations for working with gene panels or single genes (e.g., NF1) in the nf-core/rnaseq pipeline, especially regarding the use of specific FASTA and GTF files? I’ve encountered compatibility issues where tools like RSEM work fine, but STAR does not, when using gene-specific files. Would it be better not to provide specific parameters for genes and instead filter the results at the end? If so, how would that be achieved?