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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) Screen Shot 2021-04-21 at 12 47 24 PM

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...