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These transcripts with few (or no) mapped reads decrease the value of sensitivity.
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After preprocessing, the number of reads decreased to 2,957,373.
After nitrogen step-down, the antisense reads decreased as nblA sense reads increased.
The average length of the reads decreased to 315 bp after pre-processing (Additional file 1).
As a result, the percentage of uniquely mapped reads decreases, and the percentage of multiple-mapping reads increases.
The frequencies of 24 reads decreased from the 5-d seeds to the 20-d seeds, while 21 nt increased.
Because the quality of Illumina reads decreases toward the end of the reads, PANDAseq will therefore incorrectly merge reads that do not overlap.
In both the post-imputation RsaI and HincII datasets, as the number of reads decreased, small recombination events disappeared and possible artifacts began to appear.
The number of predicted functions from unassembled reads decreases abruptly at higher overlapping percentages, virtually disappearing beyond 50% (Additional file 6: Figure S4A).
The total number of aligned reads decreased by 3.7%% in the 35 bp alignment and 16.7 % in the 20 bp alignment, further reducing total base coverage.
Indeed, OTU numbers using a 96% cutoff clustering of 3000 reads decreased about 15% when compared with those using a 97% cutoff clustering.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com