Paired Reads Sequence Alignment in the NextGENe Sequence Alignment Tool
NextGENe can align paired-end/mate-paired data to a reference genome. When you load paired read sample files, NextGENe can identify the pairs only if one character, the designating character, is different between the two files, for example, 1/2 or F/R. For SOLiD system data, the designating character can also be 3/5. If Load Paired Reads is selected on the Alignment Settings page (see Load Paired Reads), NextGENe first attempts to align the reads where the gap distance (the distance between the two ends of the read in bps) falls within the expected gap distance (Library size - (2 x Read Length)). If the pairs cannot be aligned within the expected gap distance, NextGENe then aligns the reads to the best matching position. When aligning paired end/mate paired data, five results are possible (with the first four listed below being the most common):
• Both reads can be aligned to the reference and are oriented in opposite directions.
• Both reads can be aligned to the reference and are oriented in the same directions.
• One read in the pair can be aligned to the reference but the other read does not.
• Neither read can be aligned to the reference.
• Additionally, paired end/mate paired end samples often include some unpaired reads that could be matched or unmatched to the reference.
NextGENe considers each of these possibilities and provides statistics for each when aligning paired end/mate paired data.
 | If NextGENe still cannot recognize the pairs, try isolating the designating character with an underscore, for example, _1_ and _2_. |
After you complete an alignment project for paired-end/mate-paired data, in addition to the standard alignment reports (see NextGENe Viewer Reports and Tools), you can also generate specialized Paired Read reports and you can export specific information for your paired read data, such as which reads in the pair were not matched to a fasta file. All these reports ands functions are available from the Paired View menu on the NextGENe Viewer main menu. See Paired Reads Alignment Reports and Functions.