I am really having trouble doing the alignment in STAR using gff file. I tried downloading gtf files but I think finding and getting the files into cluster from Ensembl and USCS was very confusing. I was able to easily download gff files from NCBI but then using it in STAR is more complicated. I know I have to specify extra parameter for gff files and here is the code I am using:
STAR --runThreadN 12 --runMode genomeGenerate \ --genomeDir /home/n-z/valizad2/Sepsis_RNAseq/HumanData/GenomeDirectory \ --limitGenomeGenerateRAM 206609344554 \ --genomeFastaFiles GCF_000001405.38_GRCh38.p12_genomic.fna \ sjdbGTFtagExonParentTranscript Parent \ --sjdbGTFfile GCF_000001405.38_GRCh38.p12_genomic.gff \ --sjdbOverhang 100
Adding sjdbGTFtagExonParentTranscript Parent gives me the error below:
EXITING: FATAL INPUT ERROR: empty value for parameter "sjdbGTFtagExonParentTranscript Parent" in input "Command-Line-Initial" SOLUTION: use non-empty value for this parameter
I don't know why it's telling me the parameter is empty. I would appreciate your help.