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egaffo / CirComPara

:microscope: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data
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extract the circRNA sequences using the output by CirComPara #4

Closed tigerxu closed 7 years ago

tigerxu commented 7 years ago

Dear Enrico,

Sorry to trouble you for a while. I have another question. I have run CirComPara with two methods findcirc and circexplorer, several folders and a number of output files are generated. I'm not sure if outputs by circompara have a file containing the circRNA sequences. I'm wondering if there is a script or tool that can be used to extract the DNA sequences of circRNAs detected. These circRNA sequences will be used for scanning miRNA binding sites. Any advice is very appreciated. Thank you very much!

Zhuofei

egaffo commented 7 years ago

Sorry, but CirComPara does not currently predict/report circRNA sequences.

tigerxu commented 7 years ago

Many thanks for your reply! I have used the output by circexplorer to get circRNA sequences by little coding and using bedtools.