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In case multiple sequencing lanes were available, fastq files were merged before alignment.
To identify a large number of SNPs and to re-annotate the B. rapa genome, we performed deep RNA sequencing of two Brassica rapa genotypes using several tissues, environmental conditions, and treatments on multiple sequencing lanes (see Materials and Methods).
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The eight lanes of sequences were generated over multiple sequencing runs that were run to variable read lengths.
We developed a new computational analysis method showing that 1. causal genes can be identified with high probability from even a modest number of mutant genomes; 2. costs can be cut many-fold compared with a conventional genome sequencing approach via an optimized strategy of library-pooling (multiple strains per library) and tag-pooling (multiple tagged libraries per sequencing lane).
ChIP-seq samples performed in different conditions and time usually have different numbers of raw sequencing reads due to the number of sequencing lanes conducted for each sample (sequencing depth) and multiple-matched or non-matched matched reads in the sample.
A total of three sequencing lanes were run.
Dideoxy sequencing lanes are labeled.
Two paired-end sequencing lanes yielded 5,046,411 reads.
Sequencing lanes were generated from plasmids using the Sequenase 2.0 DNA sequencing kit (Affymetrix, Santa Clara, CA).
The cDNA libraries were assigned to six individual sequencing lanes, and one dedicated PhiX control lane for matrix and phasing calculations was applied during sequencing.
To quantify the effects of varying both n and sequencing depth, we simulated multiplexing n-control vs. n-treatment lanes into two sequencing lanes.
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