Hi,
This is my first post. I have used MAQ to align new sequences to a reference genome. However, I am having trouble using maqview to locate the alignments on the reference genome and I am hoping someone here can help.
I first indexed the .map file and the .cns file:
./maqindex -l 1024 -c exp.cns -i exp.map
Then I use maqview to visualize the alignments:
./maqview exp.map -c exp.cns
However, while I can see the aligned sequences and consensus sequence, the reference sequence is just XXXX. I am wondering if anyone knows why this may be happening or if I am not using the proper commands.
Any help at all will be very appreciated.
Thanks!
This is my first post. I have used MAQ to align new sequences to a reference genome. However, I am having trouble using maqview to locate the alignments on the reference genome and I am hoping someone here can help.
I first indexed the .map file and the .cns file:
./maqindex -l 1024 -c exp.cns -i exp.map
Then I use maqview to visualize the alignments:
./maqview exp.map -c exp.cns
However, while I can see the aligned sequences and consensus sequence, the reference sequence is just XXXX. I am wondering if anyone knows why this may be happening or if I am not using the proper commands.
Any help at all will be very appreciated.
Thanks!
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