Hi,
through a collaboration I got my hands on an old mate-pair dataset, generated in the pre Nextera days (MP kit v2, I am assuming). A "naive" mapping of these reads against a preliminary assembly shows that most reads are nowhere near the expected insert size of 5kb. So I was hoping to clean up the files to make sure that the reads are in fact properly trimmed/clipped and filtered. However, I have not been able to find much information how these reads are supposed to be processed, bioinformatically, so I can stuff them into e.g. Soap. Does anyone know of a tutorial/reference?
All the best,
Marc
through a collaboration I got my hands on an old mate-pair dataset, generated in the pre Nextera days (MP kit v2, I am assuming). A "naive" mapping of these reads against a preliminary assembly shows that most reads are nowhere near the expected insert size of 5kb. So I was hoping to clean up the files to make sure that the reads are in fact properly trimmed/clipped and filtered. However, I have not been able to find much information how these reads are supposed to be processed, bioinformatically, so I can stuff them into e.g. Soap. Does anyone know of a tutorial/reference?
All the best,
Marc
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