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  • CLC- extracting sequences based on coverage/length

    I'm trying to extract sequences from a reference based assembly (the reference is a transcriptome) based on coverage and length in CLC. So, I want to extract the sequences with >5x coverage and >200bp. This is simple enough for de novo assembly (extract subset), is there something like this for ref-based?

  • #2
    When you run "map reads to reference" you should selected the option "Create stand-alone read mappings" (in the last wizard step)

    The output will be table that is very similar as the the novo output and you can extract a subset.

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    • #3
      Hi
      I have a similar problem but with contigs ,I want to extract sequences between the contigs when the contigs are aligned to a refrence..how do I extract these sequences..

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