Hi,
I've been recently involved in a project where my task is to analyze double-stranded RNA sequencing data, and I'm relatively new to this field.
Data:
- Illumina MiSeq 2x150 reads
- 2 samples - about 3.5 million paired-end reads per sample
- Known linker/primer sequences
- RNA library is supposed to include only dsRNA molecules > 150 nt
I've started analyzing the data of sample 1 and I've found that a huge proportion of the reads have the following structure (R1 and R2 are mate reads):
R1-5' => [Adapter 1] [some sequence 1] [Adapter 2] [some sequence 2] [Adapter 2] xxxx 3'
R2-3' => xxx [Adapter 1] [some sequence 1] [Adapter 2] [some sequence 2] [Adapter 2] 5'
(Note 1 : mate reads are complementary)
(Note 2 : xxx portion ~10 nt long)
Is there any explanation for this?
I have a very basic idea about the RNA-Seq process, but not enough to explain why do I have more than 2 adapters per read.
Thanks in advance.
I've been recently involved in a project where my task is to analyze double-stranded RNA sequencing data, and I'm relatively new to this field.
Data:
- Illumina MiSeq 2x150 reads
- 2 samples - about 3.5 million paired-end reads per sample
- Known linker/primer sequences
- RNA library is supposed to include only dsRNA molecules > 150 nt
I've started analyzing the data of sample 1 and I've found that a huge proportion of the reads have the following structure (R1 and R2 are mate reads):
R1-5' => [Adapter 1] [some sequence 1] [Adapter 2] [some sequence 2] [Adapter 2] xxxx 3'
R2-3' => xxx [Adapter 1] [some sequence 1] [Adapter 2] [some sequence 2] [Adapter 2] 5'
(Note 1 : mate reads are complementary)
(Note 2 : xxx portion ~10 nt long)
Is there any explanation for this?
I have a very basic idea about the RNA-Seq process, but not enough to explain why do I have more than 2 adapters per read.
Thanks in advance.
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