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The top and bottom highlighted portions in grey identify reading instances that were considered anomalous with respect to their content for the temperature dataset.
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Briefly, reads were mapped to human genome (human genome v18, UCSC genome browser) using Megablast [27] to identify reads with perfect matches.
A BLAST [41] search versus the RDP database (Release 10.10) was conducted to identify reads carrying fragments of 16S rRNA genes.
The first strategy was to identify reads that matched to intronic regions.
Overlap-layout-consensus based methods [ 19- 21] first identify reads that share good suffix-prefix alignment.
It can reliably identify reads that can either be merged or need to be discarded.
The first annotation step is to identify reads of known (characterized) repeats.
Importantly, RNA-seq aligners need to identify reads that map across splice junctions.
In this study, all selected genes were manually examined in the CLC software package to identify reads showing splice sites.
Sequencing data were first filtered to identify reads significantly (p<0.05) enriched over background signal using a Poisson-based test.
In a separate but parallel process, HashMatch was used to identify reads that align to multiple locations.
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CEO of Professional Science Editing for Scientists @ prosciediting.com