|
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 %)
|
