Sequencing TruSeq Small RNA libraries

Should TruSeq Small RNA libraries be run as single-read or paired-end? Illumina recommends sequencing TruSeq Small RNA libraries should routinely be as single read (with a single index read). Paired end sequencing offers no advantage with TruSeq Small RNA libraries, as the full inserts are sequenced in a single read run.

How many cycles of sequencing do small RNA libraries need? Generally, this library type is sequenced single read, 50 bp (1x50 bp), though this can be adjusted depending on the aim of the experiment.

Why are there reads that end in adapter sequences? The inserts in these libraries are the small RNA molecules, and are often shorter than the length of the read. Reads longer than the small RNA molecules will sequence into the adapter. Data must be adapter trimmed to remove adapter content. See What sequences do I use for adapter trimming for additional information.

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