i.e. if I were to select the first 1000 reads in a fastq file of RNA-Seq data, could they be considered 1000 random reads?
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Depends on which sequencing technology you are using and where your file came from. In general ... if the reads are directly off of a sequencer then the reads will be random in terms of the molecules sequences but will be ordered in terms of where on the plate/slide/etc. the sequencing occurred. Thus if there are problems with the sequencer (bubbles, poor optics, etc.) you can see non-random effects. -
So no, the first (and last reads) in the file will usually be from the edge of the plate/slide/tile and therefore be worse quality than average.Comment
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Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
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