RNA-seq: How to know which paired reads come from the same original fragment?

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In paired-end RNA sequencing, can it definitively be known which two paired reads come from the same fragment, or is it inferred based on the distance between the reads?


RNA-Seq


Assembly

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When you go for pair-end library preparation from RNA fragments followed by its sequencing, it results in generation of 2 files, one read generated from forward sequencing (mostly denoted as R1) and second read is generated from reverse sequencing (mostly denoted as R2)

That means for each of your fragments generated during library preparation, there is 1 forward sequence in R1 and its corresponding reverse sequence in R2. So, all the reads generated from the sequencer are properly paired only having same read name/header.

extra

extra1

Here, you can see two reads, one from R1 file and second from R2 file. I.e they are representing same RNA fragment and thus they have same read name except part highlighted in red and blue which starts with 1 and 2 respectively, indicating 1st read is from R1 and 2nd read is from R2 file

You tell from the shared read name.


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