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

From: Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies

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 %)