reference genome index error

[fanchen26222]

Hello, everyone. I want to construct HBV genome index using STAR sofeware. But , the HBV annoation files (.gtf) have not exon information, so I have using the parameter "sjdbGTFfeatureExon" acoording the solution providing the sofeware. Although, the HBV index has constructed successfully, unfortunately, the HBV index only including the 9 files (Genome\Log.out\SA\SAindex\chrLength.txt\chrName.txt\chrNameLength.txt\chrStart.txt\genomeParameters.txt) and the error was exists (" could not open input file HBV_star_db//geneInfo.tab" ) when the inputfiles mapping HBV reference genome. would you give me some advise ？thankyou !

construct geneome index

fasta=./GCA_003114295.1_ASM311429v1_genomic.fna gffread -T GCA_003114295.1_ASM311429v1_genomic.gtf -o GCA_003114295.1_ASM311429v1_genomic-new.gtf gtf=./GCA_003114295.1_ASM311429v1_genomic-new.gtf STAR --runMode genomeGenerate --runThreadN 32 --genomeFastaFiles $fasta --genomeDir HBV_star_db sjdbGTFfeatureExon $gtf

mapping

STAR --genomeDir HBV_star_db --readFilesIn Q43_FRAS210204959-2r_1.clean_val_1.fq Q43_FRAS210204959-2r_2.clean_val_2.fq --runThreadN 64 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts STAR --genomeDir HBV_star_db --readFilesIn Q43_FRAS210204959-2r_1.clean_val_1.fq Q43_FRAS210204959-2r_2.clean_val_2.fq --runThrtedByCoordinate --quantMode GeneCounts STAR version: 2.7.9a compiled: 2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source Dec 05 16:56:09 ..... started STAR run Dec 05 16:56:09 ..... loading genome

Transcriptome.cpp:14:Transcriptome: exiting because of INPUT FILE error: could not open input file HBV_star_db//geneInfo.tab Solution: check that the file exists and you have read permission for this file SOLUTION: utilize --sjdbGTFfile /path/to/annotations.gtf option at the genome generation step or mapping step

[alexdobin]

Hi @fanchen26222

please send me the Log.out file from the genome generation step.

Cheers Alex