Table 2 Results of the control and the common processes of the pilot study on the PEL and ATLL samples ex-vivo samples
Pilot study | |||||
|---|---|---|---|---|---|
PEL | ATLL | ||||
Samples | HHV-8 RNA | HHV-8 DNA | HTLV-1 RNA | HTLV-1 DNA | |
HiSeq2000 run | Total reads | 144,170,345 | 118,055,719 | 171,301,521 | 154,800,548 |
Quality and hg19 filters | Remaining reads | 500,318 | 566,619 | 226,120 | 375,503 |
Control process | |||||
Mapping (bowtie2) | Nber of reads vs HHV-8 genomes | 227,842 (45 %) | 175,905 (31 %) | 0 (0 %) | 0 (0 %) |
Nber of reads vs HTLV-1 genomes | 0 (0 %) | 0 (0 %) | 321 (0.14 %) | 215 (0.06 %) | |
Similarity (blastn) | Contigs similar to HHV-8. Genome covered by contigs (%) | 22/1412 contigs (85 %) | 11/5080 contigs (92 %) | 0/1112 contigs (0 %) | 0/5463 contigs (0 %) |
Contigs similar to HTLV-1. Genome covered by contigs (%) | 0/1412 contigs (0 %) | 0/5080 contigs (0 %) | 12/1112 contigs (60 %) | 9/5463 contigs (45 %) | |
Common process | |||||
Taxonomic assignation (blastn) | Contigs without taxonomy. Total length | 118/1412 (8 %), 21,807 bases (4.5 %) | 615/5080 (12 %), 173,474 bases (9 %) | 141/1112 (13 %), 25,388 bases (9 %) | 698/5463 (13 %), 214,796 bases (10 %) |
Taxonomy count | 41 % viruses including 100 % Rhadinovirus | 80 % viruses including 100 % Rhadinovirus | 0.7 % viruses including 98 % HTLV-1 | 0.08 % viruses including 86 % HTLV-1 | |