Comparing different alignments and DGE identifying Methods
| dataset | Alignment method | method of counting | DEG identifying method | Who is working on this problem | # of DE genes |
|---|---|---|---|---|---|
| Bee | Star | featureCounts | DESeq2 | Maryam and Ambi | |
| Maize | Star | featureCounts | DESeq2 | Maryam and Ambi | |
| Bee | Hisat2 | DESeq2 | Rick and Alex | ||
| Maize | Hisat2 | DESeq2 | Rick and Alex | ||
| Bee | gsnap | featureCounts, featureCounts2 | DESeq2 | Jennifer and Kathy | |
| Maize | gsnap | featureCounts, featureCounts2 | DESeq2 | Jennifer and Kathy | |
| Bee | gsnap | EdgeR | Severin | ||
| Maize | gsnap | EdgeR | Severin | ||
| Bee | Star | EdgeR | Sathesh and Katie | ||
| Maize | Star | EdgeR | Sathesh and Katie | ||
| Bee | Hisat2 | featureCounts | EdgeR | Ryan and Siva | |
| Maize | Hisat2 | EdgeR | Ryan and Siva | ||
| Bee | Hisat2 | Stringtie/Ballgown | Siva and Jennifer | ||
| Maize | Hisat2 | Stringtie/Ballgown | Siva and Jennifer | ||
| Bee | Kallisto | EdgeR | Severin/Kyle | ||
| Maize | Kallisto | EdgeR | Severin/Kyle | ||
| Bee | Kallisto | kallisto_counts.xlsx | EdgeR | Jennifer | |
| Maize | Kallisto | kallisto_counts.xlsx | EdgeR | Jennifer | |
| Bee | Salmon | salmon_counts.xlsx | EdgeR | Jennifer/Kyle | |
| Maize | Salmon | salmon_counts.xlsx | EdgeR | Jennifer/Kyle |