Table 1.
RNA-seq alignment statistics for different combinations of the sequencing data processing steps
| Trim | Dup | RS | Total reads | properly paired (%) | singletons (%) | with mate mapped to a different chr (%) | Number of DEGs | KEGG: ECM-receptor interaction | GO: multicellular organismal process | Reactome: Transmembrane transport of small molecules | R2 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| - | - | - | 41,505,942 | 68.98+-3.71 | 16.03+-3.20 | 4.01+-3.48 | 2189 | 1.86E-07 | 8.86E-16 | 6.38E-13 | 0.6687 |
| + | - | - | 51,984,539 | 60.10+-3.68 | 10.98+-2.44 | 17.92+-3.89 | 2139 | 3.29E-08 | 2.86E-13 | 9.85E-11 | 0.6614 |
| - | + | - | 15,429,501 | 61.72+-5.45 | 12.49+-2.37 | 10.22+-4.68 | 2487 | 1.34E-07 | 2.50E-22 | 1.85E-11 | 0.6672 |
| + | + | - | 25,738,167 | 43.14+-5.77 | 7.51+-1.33 | 36.18+-5.70 | 2391 | 1.97E-07 | 4.93E-17 | 3.54E-09 | 0.6575 |
| - | - | 75 | 28,283,010 | 70.55+-3.17 | 16.74+-3.85 | 0.69+-0.09 | 2100 | 7.62E-08 | 8.85E-17 | 5.71E-12 | 0.6708 |
| - | - | 50 | 26,450,592 | 70.05+-3.24 | 17.22+-3.95 | 0.63+-0.08 | 2068 | 7.18E-08 | 1.31E-16 | 6.85E-14 | 0.6712 |
| - | - | 25 | 24,703,408 | 69.63+-3.31 | 17.66+-4.05 | 0.62+-0.08 | 2021 | 8.92E-09 | 6.33E-19 | 2.94E-14 | 0.6705 |
| - | - | 0 | 21,413,178 | 69.39+-3.47 | 18.20+-4.26 | 0.61+-0.09 | 2087 | 1.02E-08 | 3.13E-19 | 3.98E-15 | 0.6643 |
| + | - | 75 | 32,589,028 | 64.70+-3.88 | 12.29+-2.88 | 10.46+-1.82 | 2116 | 4.88E-07 | 1.12E-13 | 2.89E-12 | 0.6637 |
| + | - | 50 | 30,174,345 | 64.93+-3.92 | 12.70+-2.97 | 9.71+-1.82 | 2066 | 3.49E-07 | 2.96E-14 | 2.44E-12 | 0.6642 |
| + | - | 25 | 28,231,486 | 64.55+-4.00 | 13.04+-3.03 | 9.76+-1.87 | 2004 | 3.15E-07 | 5.05E-16 | 1.13E-13 | 0.6636 |
| + | - | 0 | 24,546,936 | 63.85+-4.25 | 13.42+-3.12 | 10.26+-2.06 | 2028 | 2.65E-07 | 3.42E-16 | 3.55E-14 | 0.6583 |
| - | + | 75 | 9,681,047 | 68.59+-4.15 | 12.22+-2.96 | 1.45+-0.25 | 2302 | 1.21E-07 | 4.18E-23 | 5.71E-12 | 0.6695 |
| - | + | 50 | 8,987,150 | 68.34+-4.18 | 12.53+-3.06 | 1.221+-0.20 | 2256 | 1.48E-07 | 4.80E-22 | 4.07E-14 | 0.6700 |
| - | + | 25 | 8,346,861 | 68.09+-4.22 | 12.83+-3.16 | 1.21+-0.19 | 2245 | 1.48E-07 | 2.70E-21 | 1.44E-14 | 0.6694 |
| - | + | 0 | 7,151,500 | 68.13+-4.26 | 12.99+-3.12 | 1.19+-0.20 | 2326 | 1.69E-07 | 2.81E-24 | 8.28E-16 | 0.6628 |
| + | + | 75 | 14,251,402 | 52.88+-6.50 | 7.54+-1.45 | 23.48+-5.56 | 2210 | 1.18E-06 | 4.34E-20 | 3.95E-09 | 0.6598 |
| + | + | 50 | 12,985,873 | 53.93+-6.45 | 7.65+-1.48 | 22.01+-5.48 | 2180 | 7.69E-07 | 5.94E-19 | 3.02E-11 | 0.6604 |
| + | + | 25 | 12,125,100 | 53.69+-6.50 | 7.81+-1.51 | 22.11+-5.58 | 2124 | 4.40E-06 | 2.98E-19 | 6.28E-13 | 0.6599 |
| + | + | 0 | 10,416,970 | 52.34+-6.98 | 7.74+-1.30 | 23.54+-6.17 | 2176 | 4.22E-06 | 3.54E-18 | 3.00E-13 | 0.6539 |
"Total reads" - average number of reads; "paired (%)" - average percent of paired reads; "singletons (%)" - average percent of single end reads; "with mate mapped to a different chr (%)" - average percent of inter-chromosome mapped reads. "Number of DEGs" - number of differentially expressed genes. To allow direct comparisons of p-values among the processing steps, the "ECM-receptor interaction" KEGG pathway, the "multicellular organismal process" GO, and the "Transmembrane transport of small molecules" Reactome pathway were selected as the most representative and most enriched functional categories in each processing step, with the full enrichment analyses results shown in Additional Files 4 and 5. "+/-" indicate whether the step (Trim - adapter trimming, Dup - duplicate removal, RS - filtering out low complexity regions with RepeatSoaker) was applied/not applied, respectively. The number in the RepeatSoaker column reflects the threshold of removing reads overlapping with low complexity regions, i.e., 75% indicates that reads overlapping 75% or more with a low complexity region were removed.