Hi, I have a problem with BBsplit. I have xenograft mouse-human rna-seq samples (paired fastq) and I had thought to using BBSplit to delete the mouse contamination.
So I used this command line:
bbsplit.sh in1=reads1.fq in2=reads2.fq ref=human.fa,mouse.fa ambiguous2=toss basename=out_%.fq refstats=Statistics_%.txt
Than, I have remapped the output fastq file for the human reference with STAR and then I would like to use FeatureCount to recostruct the rawcount of the genes, but it doesn't work well.
Can you recommend a pipeline to follow for rna-seq data after using bbsplit? Thaks so much for the reply.