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In total, approximately 61% of the genes in the B. rapa genome (25298 genes) could be mapped with unique tags (Additional file 4).

We selected the sequencing reads that could be mapped with 0-mismatch to the universal unique reads set (i.e. the tag) for our analysis.

Ideally, >30 × 10 unique reads should be mapped with <20% having to be filtered out as PCR-biased reads.

Each of these metabolic pathways was mapped with at least 200 unique transcripts.

To test this hypothesis, each probeset identified as enriched by only IVT or only WT-Pico was mapped with the BLAT tool [ 31] to a unique chromosomal location in the WS170 assembly.

In experiment 1, ~67 % of the raw reads (Table  1) could be mapped to unique loci associated with over 25,000 genes (Fig.  1), providing a large number of reads that could be further used in TSS peak calling.

Using Entrez IDs as identifiers, 4435 AR binding regions (about 67%) can be mapped to 3316 unique genes with Entrez IDs.

G1 consisted of 134,204 reads (67.88 % of the total), each of which could be mapped to one unique location with higher than 90%% coverage and identity.

Subsequently, 31,574 probe sets could be mapped to a unique genomic location with at least six perfect match probes (more than 50% of the 11 spotted probe-pairs per sequence).

Among them, 4435 AR binding regions (about 67%) can be mapped to 3592 genes with unique Refseq IDs using the closest distances of 50 kb to the TSS start or end sites as criteria, suggesting that a gene can contain multiple AR binding regions.

Using SOAP software package, about 84.7% of total past filter (PF) reads could be mapped to reference genome with unique map rate of 93.2%, and 80.8% mapped reads were located on target region.