Sentence examples for bases were mapped to from inspiring English sources
In FFPE samples, DSN-Seq and Ribo-Zero-Seq provided similar coverage profiles, where ~20% of bases were mapped to transcriptome and >60% to intronic or intergenic regions.
Using ssaha2 [ 84], repeat masked sequences with less than 100 base pairs of consecutive unmasked bases were mapped to the assembly contigs that were longer than 100 base pairs.
Compared to mRNA-Seq where 69% of bases were mapped to the transcriptome, DSN-Seq and Ribo-Zero-Seq contained significantly fewer reads mapping to the transcriptome 20-300%); in these RNA-Seq protocols, many if not most reads mapped to intronic regions.
Following the removal of adapter sequences, low-quality reads and common RNA families (rRNA, tRNA, snRNA, snoRNA), unique sequences of 18 26 bases were mapped to Rattus norvegicus precursors in miRBase 20.0 using a BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
In step 3, we collected the reads that could be mapped to the E. coli genome: (i) the first 32 bases of each read were mapped to the E. coli genome with SOAP v1 [ 57], allowing up to two mismatches; and (ii) the remaining 33rd-35th bases were mapped to the E. coli genome by forcing perfect alignments, beginning at the 33rd base and retaining the longest region that could be aligned to the genome.
A total 753 million sense and antisense reads (100 bases each) were mapped to the 37.5 Mb genome of C. cinerea O7, accounting for a sequencing output of nearly 75 billion bases (2000 times the genome size) (Table 1 and Table S2).
To perform probe level comparisons between these 50-base oligonucleotide arrays, and the 36-base oligonucleotide arrays for Rozowsky et al.'s [ 18] ChIP-chip analysis of STAT1 binding within the ENCODE region, probe intensities from the 50-base overlapping format were mapped to the 36-base end-to-end format.
Using information stored in the Ingenuity Knowledge Base (IKB), genes were mapped to genetic networks, molecular functions and canonical pathways.
One hundred base pair reads were mapped to hs37d5 using Stampy version 1.0.22 (53) (www.well.ox.ac.uk/stampy).ac.uk/stampy
Raw sequences whose last 9-14 bases represented the first 9-14 bases of the 3' cloning primer were mapped to the draft genome sequence after removal of adaptor sequences using the software SOAP [ 56].
The miRNAs from TLDA-A, which are based on mirBase v.10, were mapped to mirBase v. 20 using their corresponding v.10 sequences.
