Hi,

I am interested in checking isoform (transcript) expression in the data processed by recount3. I understand that transcript level expression is not supported by recount3. I tried to estimate the transcript level counts from the exon counts but it is not trivial.

I wonder if we can have access to the output file to retrieve the Salmon quantification file (.salmon.tsv.zst) for all the SRP datasets run through recount3? Thank you!

Best, K

Hi K,

The Salmon quantification files are not available at https://aws.amazon.com/marketplace/pp/prodview-t3rflz3f557jq or JHU IDIES SciServer. Thus they are not available from the recount3 R/Biconductor package.

Best, Leonardo