Question: Get aligment quality / identity from CRAM file (for PacBio and ONT data)
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gravatar for mschmid
2.3 years ago by
mschmid150
Switzerland
mschmid150 wrote:

I have PacBio and Oxford Nanopore reads mapped to a reference sequence. Since I have very long reads I had to use CRAM format.

Do you know a nice tool which calculates the aligment quality / mapping identity for every read from the CRAM alignment file?

Idealy it gives me also the the mapping length of the respective mapping.

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by mschmid150

How did you align the reads? Most tools able to parse BAM can also parse CRAM, so maybe Picard CollectAlignmentSummaryMetrics may do what you want?

ADD REPLYlink written 2.3 years ago by h.mon30k

Partially. But I would like to have it per read. Not an average, to be able to plot a distribution of the alignment quality.

ADD REPLYlink written 2.3 years ago by mschmid150
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