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We also mapped the reads of the indica rice variety 93-11 from Beijing Genomics Institute (BGI) against the original MSU7 cDNA sequences and the pseudo-reference.
For example, the reads of Deltaproteobacterial order Desulfobacterales (Widdel 1987), Thermodesulfovibrionaceae family from Nitrospirae (Haouari et al. 2008) capable of reducing sulfates to sulfides were identified.
Next, we aligned the reference and repaired sequence to the reads of each barcode by bowtie (version 1.1.2, http://bowtie-bio.sourceforge.net/index.shtmL) with no mismatch.
As shown in Table 1, more than 98% of the reads of each sample had a mean quality value of at least 21, which indicated that these data were reliable and that the following analyses could be performed.
If the standard deviation between the reads of a triplicate sample was above 10% the measurement had to be repeated.
The most differentially expressed contigs were selected after firstly normalising the reads of each strain to the total reads number.
Furthermore, the reads of D4* have been quality filtered, so that we only retained reads in which all bases have a high quality score.
In those cases, the reads of each contig was counted only one time.
The reads of brain and liver of each species were pooled and were assembled into unigenes.
The reads of dominant miRNAs constituted 82.7% of the total reads.
The reads of each transcript belonging to the same pathway were summed up.
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