I am am aligning my RNAseq data to a reference genome using Hisat2 for the first time and I have what I am sure is a basic question. However I am still confused after reading a number of online resources.
Broadly, my pipeline goes from FastQC to rCorrector to Trimomatic to Hisat2, and I am not certain exactly how to interpret my results.
From aligning my trimmed reads I get an output something like:
23113803 reads; of these: 23113803 (100.00%) were paired; of these: 21488690 (92.97%) aligned concordantly 0 times 753270 (3.26%) aligned concordantly exactly 1 time 871843 (3.77%) aligned concordantly >1 times ---- 21488690 pairs aligned concordantly 0 times; of these: 5618651 (26.15%) aligned discordantly 1 time ---- 15870039 pairs aligned 0 times concordantly or discordantly; of these: 31740078 mates make up the pairs; of these: 2583394 (8.14%) aligned 0 times 14947960 (47.09%) aligned exactly 1 time 14208724 (44.77%) aligned >1 times 94.41% overall alignment rate
I am a bit confused as to how to interpret these outputs and wonder if there is an 'ideal' percentage of reads that have been aligned 0, exactly 1, and > 1 time?
As well as how to interpret high overall alignment rates with high percentages of paired reads that aligned concordantly 0 times. Thank you in advance for any help!