Processing step | Elephant | Biogas | |
---|---|---|---|
Pre-processing | No. of input reads | 141,700,987 | 282,930,624 |
After removal of polyA tails and short sequences <99 | 103,591,215 | 282,711,062 | |
SortMeRNA | After rRNA removal | 77,904,289 | 274,661,662 |
Bowtie2 | Input reads | 77,904,289 | 274,661,662 |
Reads aligned 0 times | 62,293,074 (79.96 %) | 49,200,963 (17.91 %) | |
Reads aligned exactly 1 time | 12,328,533 (15.85 %) | 172,293,650 (62.73 %) | |
Reads aligned >1 times | 3,282,682 (4.21 %) | 53,167,049 (19.36 %) | |
Overall alignment rate | 20.04 % | 82.09 % | |
HTSeq-count | Counted | 8,140,194 (52.14 %) | 159,743,444 (70.85 %) |
No feature | 3,784,252 (24.24 %) | 37,124,802 (16.47 %) | |
Ambiguous | 382,196 (2.45 %) | 6,133,988 (2.72 %) | |
Too low alignment quality (MAPQ <10) | 3,304,573 (21.17 %) | 22,458,465 (9.96 %) |