Description of Further Analysis

[DarioS]

Once the user identifies differentially expressed circRNA, how can the miRNA they interact with be predicted? The IDs given to the transcripts by CIRIquant are not in some standard format such as circBase or circAtlas accept. It would be great to see a chapter in Cookbook about it.

[Kevinzjy]

You can search circ_id from CIRIquant in circAtlas through circAtlas>Data>Search circAtlas, e.g., here's the results for searching "chr2:72958136|73038438" in human.

[DarioS]

Thanks, that's good, but Network -> miRNA seems to produce no results no matter which one I try. Also, what if there are 100 circRNA that are DE between conditions? Can more than one ID be entered at a time? Search box only seems to have space for one query. Ideally, I would like to upload a CIRIquant result file and get the target miRNA of every DE circRNA in one click.

[Kevinzjy]

It seems that miRNA search in circAtlas only support input formatted as "hsa-POLL_0007" , I will reach out to our team to see if there's any solution.

[1409605824]

Hello，can CIRIquant be used to analyse the single end data? CIRI2 can analyse single or paired end data,but when i want to do differential expression of cir-RNA using CIRIquant, I find the CIRIquant just can be input paired data because of the " -1 -2 "parameter, so can you test me how to deal with it, or should i use other tools?
THANKS