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FANSe2: A Robust and Cost-Efficient Alignment Tool for Quantitative Next-Generation Sequencing Applications

Figure 5

Experimental examination of the results of FANSe2 and Bowtie2.

(A) Quantification of mRNA from A549 cells using the mapping results of FANSe2 and Bowtie2. The mRNA sequencing dataset was mapped to the human RefSeq RNA reference sequences and the quantification was performed using the standard rpkM method. (B) RT-PCR validation of mRNAs that were detected by FANSe2 but not by Bowtie2 (see Table 1). 15 µl PCR product were loaded for each lane and resolved on a 3% agarose gel. The bands with the expected product size were marked with stars. The expected product sizes were noted below. (C) RT-PCR validation of mRNAs that were detected solely by Bowtie2 (See Table 2). Two RNAs detected solely by FANSe2 (LOC647859 and PPIAL4F) were loaded as positive control. 7 µl PCR product were loaded for each lane and resolved on a 2.7% agarose gel. The bands with the expected product size were marked with stars. The expected product sizes were noted below. A faint band appeared at ∼200 bp in the lane of BCL2L2-PABPN1 but is quite different than the expected product size.

Figure 5

doi: https://doi.org/10.1371/journal.pone.0094250.g005