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- LP/VB?, 2019/02?
- version#?
- helps to detect alternative splicing
- output very nice figures
- what requirements are needed (e.g. R-3.5.1, etc.)?
- no tutorials available
- not incorporated into bcbio
- I tried it and an example of a consults is here:https://code.harvard.edu/HSPH/hbc_RNAseq_christiani_RNAediting_on_lung_in_humna_hbc02307. This packages has very nice figures: https://www.dropbox.com/work/HBC%20Team%20Folder%20(1)/consults/david_christiani/RNAseq_christiani_RNAediting_on_lung_in_humna?preview=dtu.html (see at the end of the report).
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- LP/VB/RK?, date?
- version#?
- used to call isoform switching
- not recommended - use DTU tool instead
- what requirements are needed (e.g. R-3.5.1, etc.)?
- no tutorials available
- yes, DEXseq is incorporated in bcbio
- Following this paper from MLove et al: https://f1000research.com/articles/7-952/v3 I used salmon and DEXseq to call isoform switching. This consult has an example: https://code.harvard.edu/HSPH/hbc_RNAseq_christiani_RNAediting_on_lung_in_humna_hbc02307. I found that normally one isomform changes a lot and another very little, but I found some examples were the switching is more evident.