Quick additional question about maq2sam-long. I am finding that when I move maq alignments that include paired end data into sam format I loose the unique identifiers for each of the reads. Instead, both reads of the pair end up receiving the same name. This would be fine, except that when I then export the data for use with the Integrative Genomics Viewer I can't visualize the pairing information as I would like to.
Is there a way to get maq's map files into SAM format while preserving the unique pair names and pairing information? Perhaps this stripping of unique names is appropriate and I am confused about the standard SAM format? Any help would be appreciated.
Is there a way to get maq's map files into SAM format while preserving the unique pair names and pairing information? Perhaps this stripping of unique names is appropriate and I am confused about the standard SAM format? Any help would be appreciated.
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