What is discordant read pairs?

A discordant read-pair is a pair of reads from the same fragment/insert whose alignments to the reference genome have distance and/or orientation that differ from expected if the entire fragment was contiguous on the reference genome.

What are concordant and discordant read pairs?

Concordant = read pairs that map in expected orientation & size. Discordant = read pairs that map different than what is expected.

What are discordant alignments?

A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`–fr`/`–rf`/`–ff`, `-I`, `-X`).

What are mate pairs?

Mate pair sequencing involves generating long-insert paired-end DNA libraries useful for a number of sequencing applications, including: De novo sequencing. Genome finishing. Structural variant detection. Identification of complex genomic rearrangements.

What does aligned Concordantly mean?

If reads are aligned “concordantly”, it means that they meet the expectations: usually this means that R1 is in forward direction and R2 in reverse, and the distance between the reads is in the range of 500bp.

What is a split read?

Split reads: When one portion of an NGS read map to one location and other portion of the same read map to a different location of a genome. When the read both the portions is of equal length, this is called a balanced split.

What is the difference between concordant and discordant?

Coastlines where the geology alternates between strata (or bands) of hard rock and soft rock are called discordant coastlines. A concordant coastline has the same type of rock along its length. Concordant coastlines tend to have fewer bays and headlands.

What is concordance and discordance in statistics?

Concordance & Discordance A pair is said to be concordant if 1 has a higher predicted probability than 0 and is said to be discordant if 0 has a higher predicted probability than 1 and is tied if both are same.

What is a read pair?

Paired reading is a research-based fluency strategy used with readers who lack fluency. In this strategy, students read aloud to each other. When using partners, more fluent readers can be paired with less fluent readers, or children who read at the same level can be paired to reread a story they have already read.

What is paired-end and mate pair sequencing?

Paired-end or mate-pair Follow In mate-pair sequencing, the library preparation yields two fragments that are distal to each other in the genome and in the opposite in orientation to that of a mate-paired fragment.

How do you make a bowtie2 index?

How to create a bowtie2 index database of multiple genomes?

1. # Merge all E.
2. # create bowtie2 index database (database name: ecoli)
3. # result: 6 .bt2 database files.
4. # use ‘inspect’ to check the content of your database.
5. # define your BOWTIE2_INDEXES directory and move the database files into it.

What is split alignment?

A split-alignment is a pairwise sequence alignment in which different parts of the query align to disjoint regions in the reference. Split-alignments are important in comparative genomic studies as they provide direct evidence of rearrangements such as large deletions, inversions, or chromosomal translocations.

How does paired end sequencing work?

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.

What is an example of concordant?

For example, twins are concordant when both have or both lack a given trait. Let us assume that notes standing at the same concordant interval from successive notes are in succession with one another.

What discordance mean?

lack of agreement or harmony
Definition of discordance 1 : lack of agreement or harmony : the state or an instance of being discordant. 2 music : dissonance.

What is concordance and discordance pairs in logistic regression?

What is the difference between bowtie and bowtie2?

For reads longer than about 50 bp Bowtie 2 is generally faster, more sensitive, and uses less memory than Bowtie 1. For relatively short reads (e.g. less than 50 bp) Bowtie 1 is sometimes faster and/or more sensitive. Bowtie 2 supports a “local” alignment mode, which doesn’t require that reads align end-to-end.

What is bowtie2 build?

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s of characters to relatively long (e.g. mammalian) genomes.