Questions:

1. We have DNA sequences coming from several different libraries and/or sequencing centers, each cloned with different vectors. Can I load multiple splice site files to Lucy1/2 at once to trim them all? As long as any sequence region matches any of the vector sequences it will be discarded.

2. I have ABI format files, how can I convert them into .seq and .qul files?

3. I noticed that Lucy needs a splice site file as well as the vector file, but I only have the vector file. How do I generate a splice site file based on my vector sequence?

Q: We have DNA sequences coming from several different libraries and/or sequencing centers, each cloned with different vectors. Can I load multiple splice site files to Lucy1/2 at once to trim them all? As long as any sequence region matches any of the vector sequences it will be discarded.

A: You will be losing useful information by trimming against unnecessary vectors. Ideally, you know which specific vector is used to clone your spcific sequences, and then you will trim against *only* that vector. Trimming indiscriminately against all vectors when only one of them can be the right one is not supported in Lucy1/2 but you can always run Lucy1 with a script which feeds Lucy1 with different splice site file parameters. The command line Lucy1 is available from http://lucy.sourceforge.net.
A better solution is to separate your input sequences into different subsets based on their sequence names, if possible, with each subset matching one vector used, then trim them separately with only that vector. Didn't your sequences use some naming convections that allow this identification and separation?

Q: I have ABI format files, how can I convert them into .seq and .qul files?

A: A widely used tool to generate a pair of sequence file and quality file from ABI file is Phred, you may want to check their website (http://www.phrap.com/phred/) for more details.

Q: I noticed that Lucy needs a splice site file as well as the vector file, but I only have the vector file. How do I generate a splice site file based on my vector sequence?

A: The Lucy splice site file can be generated using a plain text editor such as Notepad on PC or TextEdit on a Mac. Do not use a fancy editor like Word to edit this since it may introduce invisible characters into your file. A detailed document is included with the Lucy1 (i.e., command-line) distribution from SourceForge (http://lucy.sourceforge.net). We have here for your reference.
Please read the -vector option explanation in this document which will tell you how to construct your splice site file from your vector sequence. Even if you are just using Lucy2, there are other useful detail about Lucy1 or 2 in this document.