I want to blast my circRNAs which are identified by CIRI software to circRNAs which in circBase database(http://www.circbase.org/). how can i find new circRNAs from my identified circRNAs which are not in circBase database?
thanks!
Question: new gene discovery
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songmm19900210 • 20 wrote:
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songmm19900210 • 20 wrote:
thanks Amitm, after blast with the fasta of the Circbase data, how to discoevey new circRNA? What is the criterion?
hi,
I'm sorry I do not have any experience in interpreting circRNAs. The identification using sequences was a generic step hence replied initially. Having said that there are a few low hanging fruits you could go for if you haven't already -
- Use BLAST E-value to select high-confidence candidates. (if you have too many to strt with)
- Assuming you are working with human/ mouse, ENCODE is a wonderful resource to test hypothesis. For your high-confidence candidates, go to the UCSC browser, turn on ENCODE tracks and see if you have sign of promoter upstream (like histone marks, TFBS etc.).
- Also you could check if the region has transcription signal in other ENCODE datasets as well
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Amitm • 2.1k wrote:
hi,
Depending on the number of candidates you have, you could either use BLAST or bowtie. First you would need the fasta of the Circbase data, convert to a blast db or a bowtie index and then proceed.
If instead of fasta file, BED is available then use Galaxy: Extract Genomic DNA to get your db sequences first.
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