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Table 1 Transcriptomic sequencing runs

From: VARUS: sampling complementary RNA reads from the sequence read archive

Species

Transcriptomic runs in SRA

≤ 5% of reads align uniquely

Anopheles gambiae

597

15.5%

Bombus terrestris

357

6.4%

Chlamydomonas reinhardtii

1250

7.1%

Cucumis sativus

685

21.2%

Drosophila melanogaster

30207

22.8%

Fragaria vesca

170

10.6%

Hymenolepis microstoma

31

32.2%

Medicago truncatula

1252

9.2%

Parasteatoda tepidariorum

80

16.3%

Prunus persica

268

13.2%

Saccharomyces cerevisiae

16139

30.5%

Verticillium dahliae

30

40.0%

  1. The second column shows the total number of RNA runs in SRA for the studied species. The last column shows the percentage of runs that were sampled by VARUS of which the first batch exhibited very low unique alignability, more specifically, at least 95% of reads aligned either not at all or multiple times using HISAT2. Such runs are subsequently ignored by VARUS
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BMC Bioinformatics

ISSN: 1471-2105

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