Table 1 Bioinformatic processing of the sequence reads generated from the 6 metatranscriptomic libraries.
From: Exploring the transcriptome of Staphylococcus aureus in its natural niche
Bioinformatic filtering step | 1W | 1S | 2W | 2S | 3W | 3S |
|---|---|---|---|---|---|---|
raw reads | 46,299,650 | 47,487,990 | 9,921,650 | 41,258,105 | 59,204,687 | 114,236,035 |
reads after quality filtering | 42,037,251 | 44,693,474 | 8,972,017 | 34,585,687 | 53,143,044 | 106,548,415 |
reads after removal of human reads | 3,440,056 | 5,822,346 | 4,175,206 | 29,070,525 | 2,620,088 | 4,109,102 |
mRNA reads after removal of ribosomal reads | 2,967,566 | 3,524,160 | 2,441,919 | 8,366,998 | 1,919,599 | 2,850,659 |
reads assigned exclusively to S. aureus, similarity1 ≥80% | 5,603 | 3,544 | 33,858 | 5,1363 | 10,372 | 33,869 |
reads assigned exclusively to S. epidermidis, similarity ≥80% | 9,169 | 33,339 | 17,048 | 86,094 | 1,075 | 5,259 |
reads assigned to both, similarity ≥80% | 6,411 | 28,978 | 21,304 | 114,967 | 5,528 | 18,164 |
reads assigned exclusively to S. aureus, similarity ≥90% | 6,342 | 817 | 39,512 | 70,016 | 13,036 | 43,310 |
reads assigned exclusively to S. epidermidis, similarity ≥90% | 11,456 | 47,930 | 22,475 | 133,478 | 1,472 | 7,077 |
reads assigned to both, similarity ≥90% | 2,040 | 7,806 | 5,901 | 37,247 | 2,044 | 4,776 |
reads mapped exclusively to genes of S. aureus, similarity ≥90% | 4,853 | 583 | 30,592 | 55,517 | 10,165 | 34,984 |
reads mapped exclusively to genes of S. epidermidis, similarity ≥90% | 9,137 | 38,554 | 18,009 | 111,611 | 897 | 5,664 |
reads mapped to both, similarity ≥90% | 944 | 5,464 | 3,861 | 26,733 | 1,226 | 3,464 |
% of reads assigned to S. aureus (similarity ≥90%) that could be mapped | 73 | 70 | 77 | 79 | 76 | 80 |
