Hi, I have a basic question about RNA-seq analysis. If reads alignment rate is about 40-50% (from bowties, hisat2, or other alignment tools), would it be appropriate to increase the sequencing depth and get enough aligned reads to do analysis? Or this low alignment rate would cause some bias so we should abandon these samples? Thank you!
The sample is rice, and has high quality reference genome. I used bowtie2 to do the alignment, the summary is:
82280146 reads; of these: 82280146 (100.00%) were paired; of these: 41474464 (50.41%) aligned concordantly 0 times 12443024 (15.12%) aligned concordantly exactly 1 time 28362658 (34.47%) aligned concordantly >1 times ---- 41474464 pairs aligned concordantly 0 times; of these: 1444965 (3.48%) aligned discordantly 1 time ---- 40029499 pairs aligned 0 times concordantly or discordantly; of these: 80058998 mates make up the pairs; of these: 73562998 (91.89%) aligned 0 times 414858 (0.52%) aligned exactly 1 time 6081142 (7.60%) aligned >1 times 55.30% overall alignment rate
The reason why the rate is low is that there is condamination of some bacterium. I just want to know if this kind of reads could be appropriate for downstream analysis.