However, SOAPindel is limited in the size of detectable insertions, depending on the insert size of the reads: given our simulation parameters, we observed that SOAPindel recall decreased for insertions larger than 175 bp, and the largest insertion detected was of length 189 bp.
The repeat fragments were then cut out as BamHI fragments and inserted into a BamHI-digested UASp vector, thus generating UASp/ CTG 240/3'Eg5, UASp/ CTG 480/3'Eg5 and UASp/ CAG 480/3'Eg5 plasmids depending on the insert orientation.
Depending on the insert location, mCherry-tagged fusion proteins may terminate at different positions along the peptide.
These micro movements are in the frequency range of 25 to 29 kHz and, depending on the insert, with an amplitude of 60 to 210 μm.
The assembly of the filtered reads was done using Velvet de-novo assembly program with the velvetg main parameters: -ins_length_sd 20 -ins_length (variable, depending on the insert length) -read_trkg yes -min_contig_lgth 100 -scaffolding yes -alignments yes.
The order of paired-ends is used to annotate an inter-chromosomal cluster both as a balanced or an unbalanced translocation, and to estimate a genomic coordinate range of predicted breakpoints (the resolution depending on the insert size).
For instance, the rate of nucleotide insertion by pol β varies depending on the nucleotide inserted.
Depending on the insertion site, flanking DNA regions may partially silence the inserted promoter.
cRC values depend on the insert size for all compensation methods.
