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However, many reads that should be soft-clipped are missed for two reasons.
The 581 sequence reads contained many reads that were identical to one or more other reads.
Each read is aligned independently, causing many reads that span indels are misaligned [ 17].
Since areas such as CpG islands are dense with potential methylation sites, many reads that are of particular interest would not be aligned within realistic error tolerances.
Therefore, sequencing datasets may contain many reads that appear to be tDRs, but in fact are actually derived from full-length parent tRNA templates.
The high similarity leads to many reads that map to the reference sequences, thus making the quantification (which must process the coordinates of all mapped reads) almost equally as time consuming as the mapping process.
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However, there are many short reads that are not aligned to any known gene models.
On the other hand, the fragmentation of these DNA segments in the nucleus is expected to render many sequencing reads that will exhibit a chimeric matching pattern (discussed below).
Because of the powerful readout of RNA-seq, which can generate many sequence reads that span exon exon junctions, RNA transcripts generated from different splicing events can be identified [ 12, 13, 16].
Thus many of the reads that were not used in our assembly might contain repetitive elements.
Many of the reads that were retrieved from Sk12 had similarity to environmental organisms that contain genomic regions that are likely to be conserved across mycobacteriaceae and beyond.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com