Help with using maqview please

[lindseyjane]

I am trying to view the results of a maq analysis from the alignment file output XXX.map.

I am having trouble understanding the README file that comes with the maqview package.

I have successfully indexed the file using the maqindex command but I do not understand the instructions for the ./zrio command, or what it is doing?

Can someone help me understand what to do next please? Thanks.

[Layla]

have you converted the XXX.map file to a text file from this binary format?

[lindseyjane]

Yes, I have used the command maq mapview out.map to extract to a text file XXXX.map. I have no idea what to do next. I am quite new to using Linux and the command line so if anyone has used maqview before, please could you let me know what to do next? Thanks.

[Jonathan]

Assuming you already did the following (or similar)

./maq-0.7.1/maq fastq2bfq /tmp/s_5_1_fastQ.txt /tmp/s_5_1.bfq
./maq-0.7.1/maq fastq2bfq /tmp/s_5_2_fastQ.txt /tmp/s_5_2.bfq

./maq-0.7.1/maq fasta2bfa ./genomes/Enterobacteria_phage_phiX174/NC001422.fna /tmp/phiX.bfa

./maq-0.7.1/maq map -1 76 -2 76 -u /tmp/unusedReads.txt -N /tmp/out.aln.map /tmp/phiX.bfa /tmp/s_5_1.bfq /tmp/s_5_2.bfq

./maq-0.7.1/maq assemble /tmp/out.cns /tmp/phiX.bfa /tmp/out.aln.map

Then you could run the following:

./maqview-0.2.5/maqindex -i -c /tmp/out.cns /tmp/out.aln.map

./maqview-0.2.5/maqview -c /tmp/out.cns /tmp/out.aln.map

This will open the viewer-window, (though in this example VERY slow, as the PhiX coverage here is ~125000x, the maqview code is not build for such a coverage)

Cheers
-Jonathan

[lindseyjane]

Thank you very much for your help, it is working fine now . The problem was in fact with my maq analysis, not with my understanding of maqview.

Using the instructions for using maq on the project website the command "maq match" is used to align reads to the reference. I think this command must be obsolete because it produces an output alignment file that does not work with maqview.

The correct command you gave me to map the reads to the reference is "maq map" which I used instead and it worked perfectly. I should have noticed the "maq match" command is missing from the list of commands given when you type "maq" on the command line.

[Jonathan]

Yes, that is correct.
Glad it's working now!

Best
-Jonathan

[boccy]

Maqview crashes with mac

Hi,

I have installed Maqview 0.2.5 on my iMac and found it crashing consistently. I correcly indexed my .map file (maqindex -i XXX.map) and then run the maqview command (maqview XXX.map), I can see the main window, but after a couple of clicks it inevitably crashes complaining about a "Bus error".
Can anyone help me with this?
Thanks