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bioinfo-biols / CIRI-cookbook

Document for CIRI-series software
https://ciri-cookbook.readthedocs.io/en/latest/index.html
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Description of Further Analysis #2

Open DarioS opened 4 years ago

DarioS commented 4 years ago

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 commented 4 years ago

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. image

DarioS commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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