I have PDX RNA-seq data.I want to separate the reads of mouse and human,before comparing with tumor RNA-seq data. Is there any tool to do that?
After removing the mouse reads I want to do differential expression between primary tumors and PDX tumors.
Sorry, I have a problem with BBsplit.
I have xenograft mouse-human rna-seq samples and I had thought to using BBSplit to delete the mouse contamination.
So I used this command line:
Than, I have remapped the output fastq file for the human reference with STAR and then I would like to use FeatureCount to reconstruct the raw count of the genes, but it doesn't work well.
Can you recommend a pipeline to follow for RNA-seq data after using bbsplit?
Thanks so much for the reply.
STAR + featurecount/htseq-count is a very good pipeline to use.
I have a personal thought, if it's not correct then I'm sorry.
If you know which is the mouse and which is the human in the data, you can write shell split directly. If you don't know, you can compare it first and then split it after comparing it twice.