Maqview Reference Sequence

[unionicola]

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!

[olus]

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!

How was your exp.cns generated?
In thery the "consensus" file should contains both the assembly and the reference.
If you type:
$ cns2fq exp.cns

what happens?

Cheers