How to use MAQ's export2maq?

[cliff]

I just ran Eland on Illumina's sequence data (paired-end) and generated .export files. Then, I wanted to convert this .export file to MAQ's .map format. I checked the export2maq command:

maq export2maq [-1 read1len] [-2 read2len] [-a maxdist] [-n] out.map in.list in.export

I noticed that "File in.list consists of the sequence names that appear at the seventh column of the eland alignment file in.eland and the name you expect to see in maq alignment." Does that mean I need to generate this in.list file by myself? I used to think this .list is just the gene list file.

Also, since our experiment is paired-end design, should I put both _1_export.txt and _2_export.txt together as the "in.export"?

Thanks!

[federica torri]

I am triyng to do exactly the same thing and I set up a file similar to the example but it didn't work. Did you solve the problem? How your in.list file looks like?

Thanks

Federica

[bioinfosm]

<bump>

any comments on this issue?