Which tool/method to use for Raw data quality evaluation and filtering

Question

[arronar]

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

Thank you

Answer 1

[marina.v.yurieva]

If you just need to check qc and trim adapters/quality then the most popular QC tool is FastQC

Trimming depends on the type of reads you have (SE, PE, Hi- or Miseq). Some trimmers don't do well on Miseq because reads have different length and some don't like PEs. Sometimes you need to join the PEs and then the trimming works better.

[arronar]

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?

[michael.ante]

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.

[marina.v.yurieva]

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 :)

Answer 2

[HG]

Please have a look

http://prinseq.sourceforge.net/

[arronar]

Thank you very much, looks good.