Get nucleotide sequence of assembled RNA transcripts

Question

[drabiza1]

Is there any tool that will assemble 75 base pair reads into RNA-transcripts and give me access to the assembled nucleotide sequence?

I'm looking for chimeric and circular RNA in my sample - I used CIRCexplorer2, which has detected several candidates. At this point i would like to go to view the nucleotide sequence that has been detected in order to validate these results.

Answer 1

[tomas4482]

1. design a RNA-seq experiment specifically seuqencing non-coding RNA/circRNA sequencing.

2. subset to interested region -> extract chimeric reads from BAM using "ch" tag -> do manually blast with your candidates

I'm not familiar with circRNA. Maybe PCR or other method directly test if your candidates exists in samples should be the gold standard. If you only have RNA-seq data, you can try 2nd option. I found no tool available for such purpose. You might need to write some simple scripts. samtools alone can achieve your task I think.

[drabiza1]

Thank you for your response. I do have chimeric reads as well as a junction file - but these only have 75 bases a t a time. I'm looking to piece the junction file together with the rest of the transcript. For example, for my gene of interest I have a junction connecting exon 1 and 4 - Im looking for an assembled transcript that connects exon1 - exon2 - exon3 - exon4 - exon1

Do you think i should try a de-novo assembly?