We have mapped short-read data to a reference genome using CLC Genomics Workbench. The mapping looks good but we are unsure how to extract coverage per sites or coordinates for individual mapped reads. We would like to use this data in constructing violin plots of coverage...any ideas on how to extract and construct these figures?
IGV directly represent coverage persite
http://software.broadinstitute.org/software/igv/
Thanks Enrico...just have to figure how to get our mapped reads exported from CLC Genomics.
In which format did you export them ?
You'll need the Sorted Bam Format
http://software.broadinstitute.org/software/igv/AlignmentData
I'm asking this question mainly on behalf of a student in our group who is leading these analyses. Our filtering and mapping looks robust and makes nice figures but we are yet to discover how to export them in any format! CLC is a bit like that - the obvious functions are not always easy to find. The benefit of mapping in this environment is that it is very visually oriented - easy to scan across the genome, or segments of interest, and easy to pick up artefacts that may not be so obvious from a command line.
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