Pipeline fails if a user provides --transcript_fasta "/path/to/transcript/fasta" --additional_fasta "/path/to/spike-in/fasta" --star_index false. The error will be in the salmon quantification step and will read something like:
[2024-11-12 05:05:35.751] [jointLog] [critical] Please provide a reference FASTA file that includes all targets present in the BAM header
If you have access to the genome FASTA and GTF used for alignment
consider generating a transcriptome fasta using a command like:
gffread -w output.fa -g genome.fa genome.gtf
you can find the gffread utility at (http://ccb.jhu.edu/software/stringtie/gff.shtml)
This is because it is not obvious that transcript_fasta needs to be manually regenerated by the user for the spike-in, or left empty to be auto-generated.
Description of feature
Pipeline fails if a user provides
--transcript_fasta "/path/to/transcript/fasta" --additional_fasta "/path/to/spike-in/fasta" --star_index false. The error will be in the salmon quantification step and will read something like:This is because it is not obvious that
transcript_fastaneeds to be manually regenerated by the user for the spike-in, or left empty to be auto-generated.