Pooled alignments for all normal and tumor samples (BAM), each, along with pooled variants for all normal samples (MAF) were analyzed using MuSiC2 to calculate the background mutation rates (bmrs) for all genes, and identify a list of significantly mutated genes (p-value of convolution test ≤ 0.05; Additional file 16).
The contig pools were used to recruit reads from their Illumina HiSeq 2000 sequencing pool, by alignment to the contigs using BWA [ 61].
SHORE (Ossowski et al. 2008) was used to discover single-nucleotide polymorphisms (SNPs) in the pool by alignment to a preliminary assembly of the MTE genome (CR_stitch_Feb15th.fasta) kindly provided by Jeremy Schmutz (DOE-JGI and HudsonAlpha), Stephen Wright and Khaled Hazzouri (University of Toronto), and Adrian Platts (McGill University).
Specifically, we employed the ROC n score, calculated by pooling the alignments generated by all queries, ordered by E-value, and then considering results only up to the nth false positive [ 34].
Additional file 1: BAC pool sequencing and alignment statistics.
It does accommodate the necessary variance expected between country applications, and allows for differing local structures (Sector Wide Approaches or other funding pool mechanisms) and alignment with country planning cycles.
A. Region 10 40424001-40469000 configured with the following Genes and Transcript tracks: Pooled RNA-seq (blue gene models), Pooled RNA-seq alignments (grey bars), intron tracks for 2 cell, 1 dpf and 14 dpf (blue/green bars) and the merged Ensembl/Havana gene model ENSDART00000055339 (dark red).
Reads of BAC pool rP were aligned using Mosaik to GenomeZipper sequence dataset with the aim to optimize alignment parameters.
Sequence alignment between pools using AliBee (Table A1, E) did not identify obvious conserved extended binding motifs nor was there any homology to known AMG specific aptamers described previously.
A. Region 6 10360000-10500000 configured with the following Genes and Transcript tracks: Pooled RNA-seq alignments (grey bars) and the merged Ensembl/Havana gene model ENSDARG00000062687 (dark red).
