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I was looking pipelines to detect variant with cancer RNA-seq data (STAR-2pass bam files). After giving a look to opossum-platypus, gatk and DeepVariant pipelines I found Octopus.
Is it possible to use Octopus with RNA-seq data? The pre-processing steps are the same?
Thanks in advance,
Alejandro
The text was updated successfully, but these errors were encountered:
I am just another user, but I would suspect it would be better to use a specialised tool for this, which is designed to work with RNA-Seq data. There are many features of RNA sequencing data which make DNA variant callers inappropriate for this particular use case
As another user, it seems as though maybe one could use tools you mentioned above and then give octopus a try on just the sites other tools found? I think you would have to disable duplicate removal depending on your RNA-seq library preparation method (I.e., are there UMIs added ? For better duplicate removal in your data? ).
Hi guys,
I was looking pipelines to detect variant with cancer RNA-seq data (STAR-2pass bam files). After giving a look to opossum-platypus, gatk and DeepVariant pipelines I found Octopus.
Is it possible to use Octopus with RNA-seq data? The pre-processing steps are the same?
Thanks in advance,
Alejandro
The text was updated successfully, but these errors were encountered: