Hi,
I find myself a little confused about the diractionalityof R1 and R2 reads. The R2 is always the opposite direction of R1, but R1 can be either reverse or forward strand?
Any help/youtube clips/papers that explain this well would be highly appreciated!
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written
by
blur
2 answers
Eric Minikel's post about this might help you. But yes R1 and R2 are complimentary to each other. If you scan through your fastq files you should notice that the first read in R1 is at the same location as the first read in R2.
R1 can align in any orientation (or "be either strand", if you prefer to think of it that way (N.B., this isn't technically correct, but that's an unimportant detail for the purposes here)). R2 should have the opposite orientation.
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All sequencing always occurs in 5'-->3' orientation. Keep that in mind as you think about R1/R2 orientation.
Forward And Reverse Strand Conventions
I know the reads are 5->3, but on which strand? If my R1 is the original Forward strand, is R2 is the complementary strand? and if so, are R1 a collection of the two strands, and R2 is the complementary of each read?