I am very new to the gsMapper program and rather naive. I have used gsMapper to map our sequenced genome to a closely related reference genome. This has worked well. There was about 10% of the reads that were unmapped. A portion of the unmapped reads should represent novel sequences in our genome of interest. We have interest in identifying these novel sequences therefore I am wondering if there is an easy/straight forward approach to extract the unmapped reads and use them in a de novo assembly to get contigs of unique sequences that do not match the reference genome. We have about 60,000 unmapped reads hence I am looking for some kind of automated process.
Thanks in advance.
Chris
Thanks in advance.
Chris
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