Thus, trace file depth-sampling potentially offers a powerful and high-resolution means to estimate the copy number of particular sequences.
To analyze the coverage, scripts were written to extract global coverage data from the 454AlignmentInfo.tsv file (unique depth, column 5) and the quality of coverage at each targeted nucleotide (column 4).
From the resulting "improved" BAM files, read depth per coordinate was calculated for each accession in the discovery panel using the SAMTools depth command, and mean coverage depth per accession was calculated from the resulting coverage files (Table 1).
The input files required are as follows: a reference genome in FASTA format, Variant Call Format (VCF) files (Danecek et al., 2011) and depth files created by the 'depth' command of SAMtools (Li et al., 2009).
Additional file 1 In depth description of mRNA sequencing analysis and development of a custom microarray platform [ 20, 21, 30, 36, 48 - 69 ].
CG used three primary approaches to detect gains and losses: split-read, paired-end and read depth (File S2 and Table S3).
There was relatively good coverage of reads aligning to DLD from QTC4 (a susceptible T. castaneum population, accession JX434604) in all four treatment groups (Additional file 5), although depth of coverage was better in transcripts from the resistant insects in some regions.
The files reveal a depth of failure in the military strategy of Nato than has heretofore been evident in the media coverage of the war.
Additional file 1: In-depth interview guide for study participants.
Additional file 3 In-depth interview guide for policy makers and researchers.
See details of the guides in Additional file 1: In-depth Interview Guide; and Additional file 2: Focus Group Discussion Guide.
