Question: STAR --quantMode GeneCounts always gives 0 counts
0
mgmohsen • 0 wrote:
I'm trying to perform an alignment using STAR and extract gene count information. Here is the command I entered:
STAR --runThreadN 16 --readFilesCommand zcat --quantMode GeneCounts --genomeDir /path/to/genome/dir --readFilesIn /path/to/file_R1.fastq.gz /path/to/file_R2.fastq.gz
However, whenever I analyze ReadsPerGenes.out.tab all columns are 0 all the way down.
$ head -10 ReadsPerGenes.out.tab
N_unmapped 0 0 0
N_multimapping 0 0 0
N_noFeature 0 0 0
N_ambiguous 0 0 0
ENSG00000223972.5 0 0 0
ENSG00000227232.5 0 0 0
ENSG00000278267.1 0 0 0
ENSG00000243485.5 0 0 0
ENSG00000284332.1 0 0 0
ENSG00000237613.2 0 0 0
All of the following commands provide no output:
$ awk '$2 > 0' ReadsPerGenes.out.tab
$ awk '$3 > 0' ReadsPerGenes.out.tab
$ awk '$4 > 0' ReadsPerGenes.out.tab
In case there could be something wrong with the genome indexing, the genome was indexed using the following command:
STAR --runThreadN 16 --runMode genomeGenerate --genomeDir . --genomeFastaFiles ./GRCh38.primary_assembly.genome.fa --sjdbGTFfile ./gencode.v31.primary_assembly.annotation.gtf
Any ideas what could be going wrong here?
