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  • Can Trimmomatic handle Colorspace Reads

    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).

  • #2
    You will need to use Cutadapt: https://code.google.com/p/cutadapt/

    Comment


    • #3
      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.

      Comment


      • #4
        If you are worried about consistency then you could re-process them all with cutadapt.

        Comment

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