I have some 100nt pair end RNAseq data which is using a total RNA extraction methods from lung samples. What we try to do here is the whole transcriptome sequencing, or meta-transcriptomics.
I am thinking about assembling these reads using trinity and then map the contigs against host genome and microbial rRNA database like RDP or silva using bowtie, followed by cufflinks to do some differential analysis. How does that sound? I am looking forward to all kinds of suggestions and comments. Thank you!
I am also searching for some kind of pipeline or SOP from those who have done similar analyses before. Could some one provide me some suggestions? Any specific software package for this purpose?
Thanks a lot!