For each sample, we examine reads that overlap SNP positions from the panel to identify the base at that position.
The geneBody_coverage.py script within the RseqC package [ 59] was used to examine read coverage across gene models and test for 5′ and 3′ bias in transcript coverage.
Here, we examine read coverage on a per-locus basis in the De Bruijn graph and, once a particular locus has sufficient coverage, call errors or trim bases for all following reads belonging to that graph locus.
And yet, all of this focus on the test — which examines reading comprehension, math skills, the ability to reason logically — suggests a myopia of its own.
The primary outcome of our study was the proportion of parents who, after being exposed to the video in one of the two different periods, declared that their knowledge, attitudes and intentions regarding any of the four specific activities examined (reading aloud, exposure to music, caregiver and child early socialization) had changed.
As further evidence for contamination of the GRO-seq data with RNA not originating from nuclear run-on experiments, we examined read distributions along various non-coding RNA families.
Deakin et al. examined read errors within libraries of small numbers of barcode sequences.
To distinguish between these two options, we carefully examined reads for the presence of splice sites.
In order to reduce memory requirement, each time Pindel loads one chromosome into memory and scan the entire read alignment file, examining reads associated with the current chromosome.
In addition to compiling new junction evidence for structural variants as detailed above, breseq includes a step where it examines read coverage for evidence of deleted chromosomal regions.
This has been done by pyrosequencing [ 24], microarray hybridization [ 25], and more recently by examining read depth of SNPs using next generation sequence data (Pool-seq) [ 26].
