Read pairs mapped in forward- reverse (FR) orientation and flagged as improper pairs by BWA were extracted.
Mapped reads from each library were further filtered for duplicates, multiple mappers, improper pairs, and off-target reads.
sabaeus 1.0: GCA_000409795.1), we examined potential >1- kb-scale deletions, segmental duplications, inversions, and translocations using the information of improper paired-end mapping and split-read mapping.
Long strand assembly can be achieved in steps, as shown in Figure 2. In each step, conflicting strands (strands forming improper pairs) are separated into different tube.
Following filtering for duplicates, multiple mappers, improper pairs, and off-target reads, Chilamakuri et al. (2014) found that this platform retained fewer reads (54.8%) than NimbleGen (66%) or Agilent (71.7%).
Clusters of at least 2 improper pairs were identified where at least one end was mapped with quality greater than or equal to 20 and deletions were predicted using a custom Perl script.
They also found that out of all platforms tested, the Nextera platform retained the fewest reads after filtering for duplicates, multiple mappers, improper pairs, and off-target reads, at 40.1%.
If the joining order is improper, the conflicting pair are placed in separate tubes and a base assembly protocol is changed to a complex one.
If the batch upload procedure fails because of inconsistency in annotation or improper sequences, a pair of Excel and FASTA files containing only the erroneous entries together with a comment on the errors is returned to the user for correction and resubmission.
Here we applied Pindel that uses a split-read approach to examine unmapped reads spanning breakpoints, and BreakDancer that examines discordantly mapped read pairs having improper orientation relationships or span sizes [ 58, 59].
