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t-neumann / slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity
GNU Affero General Public License v3.0
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Downstream analysis #123

Closed paulinarosales closed 1 year ago

paulinarosales commented 1 year ago

Hi @t-neumann,

I'm using slamdunk to analyse paired-ended mRNA data (used the pertinent adjustments on the mapping step fo PE data). But I have some (rather basic) questions about DE analysis with DESeq2. I'm using both TcReadCount and ReadCount to run the DESeq2() function and then use:

sizeFactors(ddsTcReadCount) <- sizeFactors(ddsReadCount)

as described before in other issues, and use ddsTcReadCount for further analysis. Are there any other particular steps for DE analysis I should do when using TcReadCount data?

Also for gene related results I'm collapsing counts with the same transcript ID by sum() and then match with the corresponding gene ID, and use that as input for DESeq. It shouldn't be a problem right?

Sorry if my questions are far from slamdunk itself :)

t-neumann commented 1 year ago

Hi - sounds all good to me what you are doing. Typically we also filter genes for a certain baseline expression in your control condition, but that's about it. Good luck!