Recently, I have read a paper (Tiedt, S., et al. (2017). RNA-seq identifies circulating miR-125a-5p, miR-125b-5p and miR-143-3p as potential biomarkers for acute Ischemic stroke. Circulation research, CIRCRESAHA-117). Some detail of this paper is followed: PMID: 28724745 DOI: 10.1161/CIRCRESAHA.117.311572 Pubmed GEO database: SRA: SRP133275
I wanted to get the expression matrix of miRNA after stroke in human circulating blood. I got these files (SRA format) from Pubmed GEO database. Trimmed them with Trimmomatic software, and used the Hisat2 software to align the reads to the genome. However, the alignment is too low as followed.
6644136 reads; of these: 6644136 (100.00%) were unpaired; of these: 6631500 (99.81%) aligned 0 times 2981 (0.04%) aligned exactly 1 time 9655 (0.15%) aligned >1 times 0.19% overall alignment rate
Here is the shell script:
hisat2 -p 4 --dta -x ./indexes/genome_tran -U ./samples/ SRR6761159.fastq -S ./temp/ SRR6761159.sam
The indexes file is “genome_tran.[1-8].ht2”.
The alignment is too low. Does anyone have any suggestions on how to address this problem? Thank you.