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The mapping rate of the PacBio Isoform Sequencing (IsoSeq) full-length transcripts was 97.7% (Supplementary Table 5).
Mapping analysis resulted an average of 42.2 million mapped reads per sample, with an average mapping rate of 87.2% over all samples from three cohorts (Supplementary Table 5).
On average 38 ± 5.6 million reads were generated from each of the cDNA libraries using globin-reduced, unfractionated whole blood RNA, with a mapping rate of 89.8 ± 2.8% indicating high quality sequence data.
By deep sequencing of the rRNA-depleted total RNAs, we obtained an average of 211.5 million reads per sample (range from 196.6 to 229.9) with an average mapping rate of 91.7% to the reference human genome (UCSC version hg19; Supplementary Fig. 1c).
This mapping rate of bisulfite sequences was significantly higher than those obtained by Illumina short read sequencing platform, which usually varies significantly between samples [30].
An average mapping rate of ~83% (164.66 million mapped reads) was reached.
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Both total mapping rates of the two libraries were approximately 80%.
The high quality of ribosome profiling reads was evidenced by high mapping rates of cellular RPF reads in coding regions (CDSs) and 5′-UTRs as well as low mapping rates of 3′-UTRs and introns for both mock and infected experiments (Fig. S1).
Both of the mapping rates of the two libraries were almost 50%.
When mapping to the reference transcriptome, Bowtie2 obtains slightly higher mapping rates of 0.6269 to 0.7052.
Bowtie2 mapping to the reference genome (Bowtie2-G) obtains higher still mapping rates of 0.6227 to 0.6530.
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