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Refactor and test of robustness of Funnell "CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor"

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Aug 16, 2021
0db5f40 · Aug 16, 2021

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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

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Refactor and test of robustness of Funnell "CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor"

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