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To address reads back to barcodes, and hence individual PCR wells or pools, we developed a novel method based on techniques reported previously [ 16, 17].
First, we used bwa (v0.7.10) (Li and Durbin 2010) to align all clean reads back to the assembly.
The assembled transcripts were as reference sequences for transcript annotation and re-validated by aligning clean reads back to transcripts (Miller et al. 2012).
We mapped reads back to reference genomes by means of BLAST search [33].
Here we present a novel strategy where the combination of two tags is used to link sequencing reads back to their origins from a pool of samples.
The mapping step maps the reads back to the reference genome.
In all cases, we mapped reads back to the final assembly contigs.
This phenomenon was observed by mapping the clean reads back to pre-miRNAs (Table 1).
This maps the reads back to the assembled transcripts using the bowtie aligner.
When aligning the genomic reads back to the de novo assembly, 3.6 million reads aligned.
By mapping reads back to contigs and combining paired-end information, contigs were linked into scaffolds.
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CEO of Professional Science Editing for Scientists @ prosciediting.com