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The assembled transcripts were as reference sequences for transcript annotation and re-validated by aligning clean reads back to transcripts (Miller et al. 2012).
When used to determine gene expression profiles, the generated sequence reads are mapped back to transcripts.
Bowtie2 (version 2.1.0) were used to align preprocessed reads(clean reads) back to transcripts, in order to get assembly statistics.
Therefore, when mapped back to transcripts, the reads mapped to the sense strand and antisense strand of transcripts are equally summarized without discrimination.
We mapped the NGS sequence reads back to transcripts to classify the sequence reads, mappable or unmappable, and to determine gene expression profiles.
The de novo assembly was performed by the CLC Genomics Server using the scaffolding option and the mapping reads back to transcripts option.
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When mapping female genomic reads back to male transcripts, four Muller C transcripts had zero female genomic read coverage, indicating that these genes are not present in the female genome.
We then determined the RPKM values of the transcripts by mapping the sequence reads of SS and NSS libraries back to the transcripts, followed by calculating the correlation coefficient of RPKM values of the two libraries (see Section 2).
Any discrepancies in codes were resolved via consensus, referring back to the transcripts and discussing codes until there was 100% agreement on designated codes.
Large number of the reads (91%) aligned back to the transcripts as expected (Table 4).
The individual sets of reads were then mapped back to the transcripts using BWA 0.5.8a [ 76].
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