snakemake --no-shared-fs --default-remote-provider S3 --default-remote-prefix clk \
clk/SRP091981/untreated_vs_0.05.manifest.txt clk/SRP091981/untreated_vs_0.1.manifest.txt clk/SRP091981/untreated_vs_0.5.manifest.txt clk/SRP091981/untreated_vs_1.0.manifest.txt
Here I reproduced the differential isoform usage induced by T3 using rMATS, rMATS-ISO, SUPPA2, and (the original paper used GSNAP/MISO/Cufflinks)
| Original implementation | #1 | #2 | #3 | |
|---|---|---|---|---|
| Aligner | GSNAP | STAR | Salmon | |
| Genome | GRCh37 | GRCh38 | GRCh38 | GRCh38 |
| Differential Splicing | MISO | rMATS | SUPPA2 | |
| Isoform Detection | rMATS-ISO | |||
| Conjoined gene detection | deFuse | ARRIBA |
Reviewers are free to alter whatever they choose in order to assess the validity of this study.
Some suggestions include, but are not limited to...