Can Trimmomatic handle Colorspace Reads

[Fernas]

I have a RNASeq fastq file (first 4 lines are):
=====
@SRR179591.1.1 mendel_20110320_FRAG_BC_Ryan_RNA_Seq_2_58_235_F3 length=50
T.33.2010.0313.1231222320.1.3312.0.12.0212.0.013000
+SRR179591.1.1 mendel_20110320_FRAG_BC_Ryan_RNA_Seq_2_58_235_F3 length=50
!!A+!@>A5!@59%!=A'6=4@5'A!9!55=1!(!0-!'%-%!&!%&%60'
=====

This fastq format is Color-space. I am wondering if Trimmomatic can handle such file by trimming reads based on quality and adapters?
(I did not see in the documentation of Trimmomatic that it can handle Color-space reads).

[GenoMax]

You will need to use Cutadapt: https://code.google.com/p/cutadapt/

[Fernas]

Thank @GenoMax.
Actually, I have 100 fastq files. 95 of them contain quality values encoded in Phred33 (so I processed them with Trimmomatic), while 5 files are Color-space. I wanted to use Trimmomatic for all the 100 files for simplicity but it seems that I need to process those 5 files with Cutadapt.

[GenoMax]

If you are worried about consistency then you could re-process them all with cutadapt.