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Hi Viktor,The general recommendation from both the Salmon and DESeq2 developers here is to not do this. The recommended pipeline is to provide the transcript level quant.sf files to TxImport and then to provide the TxImport object containing both estimated count and transcript length information to DESeq2. We've implemented that pipeline in the tximport.DESeq2 module available here: https://cloud.genepattern.org/gp/pages/index.jsf?lsid=urn:lsid:8080.gpserver.ip-172-31-26-71.ip-172-31-26-71.ec2.internal:genepatternmodules:179:3.2.3That module has a warning about it being specifically for a workshop, but it should work well enough for general use.If you only have the gene level quant.genes.sf files, then you could probably use the counts with DESeq2, but again, that isn't really recommended. I can't remember if our module automatically rounds the counts in that case or would error if the counts are not integers (which is the default DESeq2 behavior).-AnthonyAnthony S. Castanza, PhDMesirov Lab, Department of MedicineUniversity of California, San Diego
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