Extension of reads into fragments

ChIP-seq libraries consist of fragments of amplified DNA that represents the purified material. These fragments are often 100 -250 bp long, and in a typical NGS sample only a part (e.g. 50 bp) of this is sequenced. Consequently, reads on the sense and antisense strands will be 100-250 bp apart in a typical Dataset. Therefore, EaSeq assigns a DNA fragment length to the reads during import (default is 150 bp), and the user can enter custom values that are based on experimental analysis. This value can also be determined computationally and/or changed after import, but the value will be uniform for the entire Dataset, so you cannot currently have a population of fragments ranging from e.g. 80-350 bp. EaSeq can be instructed to extend the fragments from the start, end or center of the reads, but that is an option that is rarely changed from the default for common formats. Fragments will be extended depending on whether they are on the sense or antisense strand, and a sense read will be extended towards increasing values, whereas an antisense read will be extended towards decreasing values.