Hello. I'm studding about RNASeq and specifically about differential expression techniques/pipelines. As anyone knows, the first step is to evaluate and filter the raw data. Actually there are tons of tools and papers evaluate them out there for this step. Here is a list of them in wikipedia. As also and some papers describing them. Paper 1, Paper 2.
The question is, which one to choose? Which one is the most used tool for that step using Illumina data?
Any idea or hint will be welcome
As I understood, FastQC only checks the condition of the raw data, it cannot edit them (remove adaptors and filter low quality reads). So which tools are those that helps you trim and fix your library?
In general, I also use the FastQC tool.
For the trimming it depends on the data, as Marina wrote.
For simple trimming (SE, not too long) and adapter removal operations, I stick with the good old FastX tools.
For more complex reads (e.g. PE), I use bbduk from the bbmap tools.
yes, I personally use trimming tools implemented into Pipeline Pilot (but it's a commercial software). FastX work fine for simple reads as Michael said but can get freaky on PEs or on reads with different read lengths. Haven't tried bbmap, might be a good alternative though :)