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Old 11-09-2012, 10:19 AM   #1
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Default clc exporting mapped reads

After mapping some Illumina short-reads back to a reference, I want to be able to export the reads that were successfully mapped for use in mapping to a different reference. For the unmapped reads, this seems possible to do as you can set them aside in their own list as part of the mapping results. Any suggestions for manipulating a list of mapped reads within CLC or exporting them for use in a different program?
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Old 11-09-2012, 11:25 AM   #2
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Probably more than one way to do this but here is one:

1. Open the aligned sequence dataset by double clicking.
2. In the graphics window that opens, "right click" on the image somewhere in the region that shows the alignments and then Choose "Extract" Sequences.
3. That will create new entries for the sequence(s) in the navigation area. Single and paired end sequences are saved as separate datasets with "extracted sequences" as part of the name.
4. Select the newly created dataset(s) in the navigation area and then choose "export".
5. Select the format to export (e.g. fasta, fastq and others) to local storage.

Last edited by GenoMax; 11-09-2012 at 11:28 AM.
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Old 11-09-2012, 12:48 PM   #3
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I also got a reply from CLC's support guys:
You can export all reads from a read mapping via the Extract Sequences tool (under Toolbox | Classical Sequence Analysis) -> General Sequence Analysis -> Extract Sequences (Image extractsequences)).

To do this, select the read mapping from which you would like to extract the reads in the Navigation Area, and run the tool. You can find more information on the Extract Sequences tool in this section of our online manual (, or in section 11.7.3 of the pdf manual.

Best wishes,

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clc, illumina, read-mapping

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