Hi,
I used HISAT2 to align human RNA-seq data (Illumina PE, Stranded, rRNA depleted).
We are interested in comparing gene expression levels, snp and different isoform usage between treatment conditions in the end.
I got about 70-75% reads aligned concordantly 1 time and about 20% concordantly >1 time with less than 10% disconcordantly aligned. Overall mapped rate is over 95%.
Is there a common benchmark that how much % unique concordantly mapped reads is typical for human RNA?
I'm wondering how to determine whether alignment result is acceptable for carrying on the downstream analysis and how I could tweak with the parameters in HISAT if needed.....
Thank you,
I used HISAT2 to align human RNA-seq data (Illumina PE, Stranded, rRNA depleted).
We are interested in comparing gene expression levels, snp and different isoform usage between treatment conditions in the end.
I got about 70-75% reads aligned concordantly 1 time and about 20% concordantly >1 time with less than 10% disconcordantly aligned. Overall mapped rate is over 95%.
Is there a common benchmark that how much % unique concordantly mapped reads is typical for human RNA?
I'm wondering how to determine whether alignment result is acceptable for carrying on the downstream analysis and how I could tweak with the parameters in HISAT if needed.....
Thank you,
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