Identifying introns
2
0
Entering edit mode
8 weeks ago

Hello everyone

I have very basic question. I have RNA sequencing data and I would like to identify the intronic sequences. Does the RNA-seq data have both introns and exons? When I googled, it says that RNA-seq data has exon-exon binding. My question is how to obtain the intronic sequences from RNA-sequencing data ?

Thanks

RNA-Seq • 252 views
ADD COMMENT
2
Entering edit mode
8 weeks ago

Does the RNA-seq data have both introns and exons?

That depends on the type of RNA-seq library preparation that was done. Some prep kits exclude immature RNA (which would contain introns), other kits do not. This paper by the Griffith brothers has some good explanations on the different types of RNA-seq data that can be generated, specifically this image might be helpful for your question at hand.

how to obtain the intronic sequences from RNA-sequencing data ?

As the other answer indicates, you simply have to align the reads to the full genome which will include intronic, exonic and non-genic regions. If your data contains intronic sequences, those will align to the annotated introns.

ADD COMMENT
0
Entering edit mode

Thank you so much for your response.

ADD REPLY
1
Entering edit mode
8 weeks ago
Zhilong Jia ★ 1.9k

mapping the reads to reference genome with annotation, which includes the intron locations in the genome.

ADD COMMENT
0
Entering edit mode

Thank you so much for your response

ADD REPLY
0
Entering edit mode

A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.
upvote_bookmark_accept

ADD REPLY

Login before adding your answer.

Traffic: 1726 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6