Hi,
I have a slightly weird question about paired end reads. I will try to explain as best as I can:
For simplicity, let's assume that the read length is just 3 base pairs. Let the DNA fragment being read have the sequence AGCTAAGGTCG.
With paired end reads, my understanding is that we will read the first three (AGC) and last three (TCG) bases of this sequence, with the middle section (TAAGG) unknown.
With the common data formats used to represent paired end reads (FastQ etc), how is the pair represented? Are the two pairs shown as AGC and TCG (both reads running left to right on the original sequence) or as AGC and GCT - the "left" read running from left to right and the "right" read running from right to left, presumably the direction in which the two reads were extracted?
I guess what I am asking is: Is there a directionality to the reads? Are all reads represented in the same "direction" as related to the genome from which they were extracted? Does this apply to the two pairs of a paired end read?
Please let me know if I am not making any sense at all :-)
I have a slightly weird question about paired end reads. I will try to explain as best as I can:
For simplicity, let's assume that the read length is just 3 base pairs. Let the DNA fragment being read have the sequence AGCTAAGGTCG.
With paired end reads, my understanding is that we will read the first three (AGC) and last three (TCG) bases of this sequence, with the middle section (TAAGG) unknown.
With the common data formats used to represent paired end reads (FastQ etc), how is the pair represented? Are the two pairs shown as AGC and TCG (both reads running left to right on the original sequence) or as AGC and GCT - the "left" read running from left to right and the "right" read running from right to left, presumably the direction in which the two reads were extracted?
I guess what I am asking is: Is there a directionality to the reads? Are all reads represented in the same "direction" as related to the genome from which they were extracted? Does this apply to the two pairs of a paired end read?
Please let me know if I am not making any sense at all :-)
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