I am having low unique mapped read. I am a beginner and I might have done any mistake.
So first I downloaded a reference genome file and annotation file from ensemble.
then I did genome indexing with the following code
STAR --runThreadN 64 --runMode genomeGenerate --genomeDir STAR_folder --genomeFastaFiles Mus_musculus.GRCm39.dna.toplevel.fa --sjdbGTFfile Mus_musculus.GRCm39.103.gtf
Next the alignment was done for this sample SRR1552444.fastq.gz
With this code:
STAR --genomeDir STAR_folder/ --readFilesIn SRR1552444.fastq.gz --readFilesCommand zcat --outFileNamePrefix STAR_Align/444_ --outSAMtype BAM SortedByCoordinate --runThreadN 16 --sjdbGTFfile Mus_musculus.GRCm39.103.gtf
The problem was that the unique mapped reads were only 15% and from literature it is a least 75 %
Do you know where the mistake might be?