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If you have any questions that have not been answered here, please contact us.

What is SpliceMap?

SpliceMap is a program written entirely in C++ that is able to discover splice junctions from RNA-seq data. It also computes the coverage at each location and functions as an aligner.

Does SpliceMap support FASTQ format?

Yes, as of version 3.2 it does! However, it does not yet preserve read quality. This will be added in the next version.

Does SpliceMap output in SAM format?

Yes, as of version 3.1.1 it does!

Does SpliceMap support reads in colorspace?

No, not yet. If there is high demand, we will look into it.

What is Eland and how do I obtain it?

Eland is a short reads mapper that is provided if you are a user of Illumina(tm) devices. As a result, we cannot include this tool in the package. However, we do provide some instructions on how to configure it if you do have the Eland software. Please contact us if you are licensed to use Eland and we can provide you a pre-compiled copy.

What is Bowtie and how do I obtain it?

Bowtie can be found here.