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  • Joelvet
    replied
    plz try Prinseq-lite and Tag cleaner to trim ends of your reads

    Leave a comment:


  • KatrinSameith
    replied
    Dear vishnuamaram and Weilong,

    Thank you for your replies. I will try fastx_clipper or cutadapt to trim one-sided first (I am dealing with adaptor sequences) and then run --end-to-end alignments.

    --local alignments was my first idea, because I thought I would circumvent the trimming step. But never mind, it makes sense and it seems to be required.

    Thanks again & have a nice day,
    Katrin

    Leave a comment:


  • gwl186
    replied
    Originally posted by KatrinSameith View Post
    Hi Weilong,

    did you find a way around your problem? I am facing a similar question, so I push your post up again. Is it possible for --local alignments to just trim the 3' end?

    Would be happy for any advise! Thanks in advance.
    Katrin
    Hi KatrinSameith,

    Not yet. I haven't find any way to get around the problem only using bowtie2. Maybe other tools could be used to get around this. Such as Vishnuamaram's suggestion.

    Weilong

    Leave a comment:


  • vishnuamaram
    replied
    Hey KatrinSameith,

    Try using FASTXTOOLKIT, with this you can specifically trim.

    Leave a comment:


  • KatrinSameith
    replied
    Hi Weilong,

    did you find a way around your problem? I am facing a similar question, so I push your post up again. Is it possible for --local alignments to just trim the 3' end?

    Would be happy for any advise! Thanks in advance.
    Katrin

    Leave a comment:


  • gwl186
    started a topic Bowtie2 limit local alignment to 5' end

    Bowtie2 limit local alignment to 5' end

    Hi all,

    I'm using bowtie2 to do the local alignment. However, we are thinking the 5' end will have enough good sequencing quality, while 3' end may not. We are trying to use local alignment option to map the reads. However, I found the result will allow soft trimming on both 5' and 3' end. Could I only limit it to only allow trimming on 3' end but not 5' end? I didn't find any option in bowtie2.

    Do anyone have suggestions for me to do this?

    Best, Weilong

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