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Question about trimmomatic

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  • Question about trimmomatic

    Hi,

    I'm a first time user to trimmomatic and I have paired-end RNA seq data. My question why do I get paired and unpaired output for each read at the output?

    java -classpath <path to trimmomatic jar> org.usadellab.trimmomatic.TrimmomaticPE [-threads <threads>] [-phred33 | -phred64] [-trimlog <logFile>] <input 1> <input 2> <paired output 1> <unpaired output 1> <paired output 2> <unpaired output 2> <step 1>

    I have used CLC genomics for trimming and using that I'll get two output files namely read1_trimmed.fastq and read2_trimmed.fastq. Why do I get 4 output files in trimmmomatic?

  • #2
    I got the answer from Federico.

    the answer is: because Trimmomatic doesn't discard unpaired reads, as CLC does.
    Trimmomatic trims both reads in a pair. If one of the reads is of high quality, and the second one is of low quality, only the first is kept. This may happen in cases when the two sequencing cycle groups have generally different noise levels (recently, it happened in our institute that the laser died during the second cycle, and trimming removed most of the _2 reads, allowing us to keep the _1).

    Most of the other non-CLC trimming tools do the same as Trimmomatic. If you really don't want them, you can ignore _U1 and _U2. Trimmomatic just give you an extra chance to use your unpaired sequences.

    Federico

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    • #3
      For assembly which reads should be used? paired one or unpaired...

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      • #4
        Originally posted by Rahul shelke View Post
        For assembly which reads should be used? paired one or unpaired...
        You can use both. Depends on the assembler.

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