Exporting QSeq Data for Use in SeqMan NGen

QSeq data can be exported for assembly and downstream analysis in SeqMan NGen, DNASTAR's software for performing next-gen sequence assembly:

1)  Open a QSeq project in ArrayStar.

2)  Display Gene, IP Peaks, or IP Fragments.

3)  Select some or all of the data in all views.

4)  Choose Data > Export Sequences.

5)  In the Export Sequences dialog, check both Export matching reads and Launch NGen afterwards.

6)  Click Export. SeqMan NGen will launch automatically.

The following outputs will be created:

•      A GenBank or FASTA file containing sub-sequences (or fragments) of the original QSeq template. (Selecting GenBank will preserve annotations, while FASTA will not.) The fragments will be the portions matching each selected peak, fragment, or gene in the project. You can find what sub-sequence this will be by looking at the Source Sequence and Source Range annotations.

•      A FASTQ file containing the reads which have at least partial matches to these sub-sequences out of the read files you select in the dialog.

•      A SeqMan NGen script (which opens in the SeqMan NGen wizard after you click Export) directing the application to assemble the reads from the FASTQ file (#2) against the GenBank or FASTA template (#1).