What is paired-end sequencing?
What is Paired-End Sequencing? Paired-end sequencing allows users to sequence both ends of a fragment and generate high-quality, alignable sequence data. Paired-end sequencing facilitates detection of genomic rearrangements and repetitive sequence elements, as well as gene fusions and novel transcripts.
Is ChIP seq paired-end?
Sample preparation and sequencing Single-end reads are often used for typical ChIP-seq analyses, while paired-end ones improve the library complexity and increase mapping efficiency at repetitive regions [38].
What is the difference between single-end and paired-end sequencing?
In single-end reading, the sequencer reads a fragment from only one end to the other, generating the sequence of base pairs. In paired-end reading it starts at one read, finishes this direction at the specified read length, and then starts another round of reading from the opposite end of the fragment.
What is paired-end mapping?
End-sequence profiling (ESP) (sometimes “Paired-end mapping (PEM)”) is a method based on sequence-tagged connectors developed to facilitate de novo genome sequencing to identify high-resolution copy number and structural aberrations such as inversions and translocations.
How do I join paired-end reads?
To merge paired reads, select one or more sequence list documents and go to the Set & merge paired reads option in the Pre-processing dropdown. Depending on your sequencing data, reads could be in parallel sets of sequences or interlaced, so you will need to specify which format should the reads be paired by.
How to optimize performance of DNase-seq?
We studied the key experimental parameters to optimize performance of DNase-seq. Sequencing short fragments of 50–100 base pairs (bp) that accumulate in long internucleosome linker regions was more efficient for identifying transcription factor binding sites compared to sequencing longer fragments.
What is the difference between DNase-seq and FAIRE-seq?
DNase-seq ( DNase I hypersensitive sites sequencing) is a method in molecular biology used to identify the location of regulatory regions, based on the genome-wide sequencing of regions sensitive to cleavage by DNase I. FAIRE-Seq is a successor of DNase-seq for the genome-wide identification of accessible DNA regions in the genome.
Can DNase-seq detect TF binding sites?
To optimize DNase-seq and to characterize its biases, we studied the key parameters of DNase I concentration and selected fragment size. We assessed the ability of DNase-seq to detect TF binding sites and to understand systematic biases that could influence interpretation of DNase-seq data.
How informative is DNase-seq data from genome-wide binding sites?
In our analysis of the genome-wide binding sites of 36 TFs, we found that although footprinting data from DNase-seq were informative for some TFs such as CTCF, such data were uninformative for many others such as the androgen receptor (AR).