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Old 11-20-2013, 09:31 AM   #1
Location: Canada

Join Date: Oct 2013
Posts: 14
Default 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?
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Old 12-02-2013, 11:59 AM   #2
Patrick Dekker
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Location: Netherlands

Join Date: Oct 2008
Posts: 5

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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Old 07-15-2015, 12:25 PM   #3
Location: new mexico

Join Date: May 2015
Posts: 17

I have a similar problem but with contigs ,I want to extract sequences between the contigs when the contigs are aligned to a do I extract these sequences..
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