Table 5 RNA-Seq processing steps and number of cDNA sequence reads obtained for elephant feces and biogas fermenter samples

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 %)