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  • TopHat - Bowtie read trimming

    Hello:

    I am using TopHat for aligning RNA-Seq reads and map exon junctions.

    I am familiar with BWA and skimming through Bowtie (that tophat uses for alignment) and wondering if Bowtie has quality trimming option.

    Something similar to BWA aln -q option. Here -q removes the 3' bases if the quality is below a threshold.

    bwa aln -q 20 mysamp.fastq

    my fasta reads 3' ends have very low quality bases.

    thanks
    Adrian

  • #2
    Why not use an external filter? For example, here's a simple Biopython scirpt to filter reads that have quality below some fixed value.

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    • #3
      Sangenix : Can perform Trimming of reads based upon Quality Score

      Sangenix Qc and Trimming option , can remove the low quality filter , based upon user input in an auto mated way. Minimal user interference for execution of workflow and excellent result output


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