Entering edit mode
5.0 years ago
drragill
▴
10
Hi, I wanted to detect the Tandem repeat elements from the RNA-Seq data and then my aim to find the regulatory sequences from this. Please tell me which software I should use and also tell me if there is any such database exists. Thanks!
Some background would help. Do you have a reference genome/transcriptome. Which species? How did you sequence your libraries in terms of read length? Do you plan to do any assembly or do you already have a reference? If so:
SSR marker discovery from RNA-seq data when a reference genome is available
Thanks for your kind reply, yes I have a reference genome. My Species name is Brassica napus and genome already been sequenced. Actually, I found a pipeline to obtain the TE (Transposable elements) using RNA-seq data. As I read in the literature, TE produced all non-coding gene regulators such as lncRNAs, small RNA species, and cis-regulatory sequences. As we know repeat elements are TR and TE, so my aim to find these above non-coding gene regulators using my RNA-Seq (Q30:95-96%, it is a good quality read using Illumina, Hiseq Xten) data via TR (tandem repeats) and TE. I have also found some literature (database) in which they tell the pipeline of obtaining non-coding RNAs from TE. But, I could not find the cis-regulatory (enhancers and promoter sequences) elements. Also, I could not find the literature to find TR using RNA-Seq data. I am working on the Abiotic stresses especially heavy metals and I wanted to explore the response of these TR and TE and their offspring related to external environments. And how these all elements co-expressed in a network. Many thanks!
Although there are exceptions, the majority of tandem repeats are in non-coding regions, and will therefore not be sequenced in your RNA-seq experiment. In addition, regulatory sequences are also mostly non-coding. Why do you think RNA-seq is an appropriate technique for your research question?