Table 4.
Bioinformatics pipelines and gene models used for RNA-Seq data analysis
| Data set | Pipeline | Aligner | Counting and normalization | Reference genome | Gene annotation | Mapping approach |
|---|---|---|---|---|---|---|
| SEQC NB | P2 | Novo align v2.08.01 | Global scaling to RPM | UCSC hg19 | Human RefSeq RNA v51 | ID mapping |
| NCTR rat toxicogenomics [20] | P2 | Novo align v2.08.01 | Global scaling to RPM | UCSC rn4 | Rat RefSeq RNA v52 | Location mapping |
| SEQC main [16] | P2 | Novo align v1.7.01 | Global scaling to RPM | UCSC hg19 | Human RefSeq RNA v51 | Location mapping |
| SEQC rat toxicogenomics [22] | P1 | Magic | Magic index | RGSC v3.4 | Ace View 2008 gene models | ID mapping |
| P2 | Novo align v2.08.01 | Global scaling to RPM | UCSC rn4 | Rat RefSeq RNA v52 | ID mapping | |
| P3 | Bwa 0.5.9-r16 | Samtools 0.1.13 | Rat RefSeq RNA v50 | ID mapping | ||
| P4 | To phat | HTSeq-count 0.53p3 | UCSC rn4 | Rat RefSeq RNA v50 | ID mapping | |
| P5 | Bowtie v0.12.7 | RSEM v1.1.18 | Ensemble rat genome 66 | Ensemble genes build 66 | Location mapping | |
| P6 | To phat 2.0 | Cufflinks + Cuffdiff | UCSC rn4 | Cufflinks de novo assembly | Location mapping | |
| TCGA AML [17] | Bwa 0.5.7 | In-house program | hg18 + exon junction | Ensembl v59 | ID mapping |