[greigite]

I just assemble my solexa data with velvet, and get about 240 contigs larger than 500. Then, I map the solexa data to the contigs using the consed/addSolexaReads.perl to get a contigs with quality. Now, I want to convert the ace file to phd file individually. The consed can export the phd file only one at a time, I just want to know how to convert it all at a time.

If you want to get the consensus contig sequences as phd files you could export all contigs from Consed into a multifasta, then use lib2Phd.perl to convert them into phd files. You'd have to write your own script to get the consensus contig qualities into the fake phd files as lib2Phd.perl just puts a score of 20 for all bases.
If you wanted to get your solexa reads into phd files you could also use lib2Phd.perl on the read fasta file, then write your own script to pop Solexa qualities into these fake phd files. I did this with 454 reads and it works well to visualize read qualities in Consed.

[anyone1985]

Thanks. I am trying.......

If you want to get the consensus contig sequences as phd files you could export all contigs from Consed into a multifasta, then use lib2Phd.perl to convert them into phd files. You'd have to write your own script to get the consensus contig qualities into the fake phd files as lib2Phd.perl just puts a score of 20 for all bases.
If you wanted to get your solexa reads into phd files you could also use lib2Phd.perl on the read fasta file, then write your own script to pop Solexa qualities into these fake phd files. I did this with 454 reads and it works well to visualize read qualities in Consed.