Riboseq multi stage mapping and filtering - wdlingit/cop GitHub Wiki

This is an index page pointing to parts of a complete procedure that we applied to a number of Riboseq read datasets for mapping them to the arabidopsis genome. In the procedure, we tried leveraging on existing genome annotation and supports from available RNAseq datasets. Given that reads been adapter clipped by tools like cutadapt and not filtered by rRNA read removal tools like sortmerna, the procedure used to map our Riboseq read datasets to the arabidopsis genome with mapping ratios more than 90%.

Please note that, in all parts, there might be numbers of perl oneliners been applied. All perl oneliners work as simple scripts and there should be almost no needs to modify them. We used to save them in our process log so that necessary modification can be done without saving a large number of scripts for all different practices of our data processing.

Refer the environment setting for most of used tools. Please raise an issue if there is any questions.

0. Database construction
1. Adapter removal and read multiplexing
2. Multi stage mapping
3. Filtering and read demultiplexing
4. Expression level computation