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Old 04-16-2013, 09:18 AM   #1
bob-loblaw
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Default Does RNA-Seq sequence randomly?

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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Old 04-16-2013, 09:53 AM   #2
westerman
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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.
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Old 04-16-2013, 10:34 AM   #3
maubp
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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.
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Old 04-17-2013, 02:33 AM   #4
bob-loblaw
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Quote:
Originally Posted by westerman View Post
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.
Okay thanks, it was an illumina hi-seq machine
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