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TreesLab / CircMiMi

A package for constructing CLIP-seq data-supported circRNA-miRNA-mRNA interactions
MIT License
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Question about start coordinate #6

Open algaebrown opened 7 months ago

algaebrown commented 7 months ago

Hi TreesLab,

Thanks for creating such an awesome tool. I wonder for the "start coordinate pos1" in CIRC_FILE, which system should the annotation be in? Each circle tool report the start coordinate slightly differently (1bp difference). Not sure if this will affect the result from CircMiMi?

For example, if a circRNA is derived from chr1:1000-2000, it should be reported as chr1:1000-2000 in CIRI-series and some tools (DCC/KNIFE/Mapsplice), but reported as chr1:999-2000 in other tools (CIRCexplorer2/UROBORUS/circRNA_finder/find_circ). (ref: https://ciri-cookbook.readthedocs.io/en/latest/CIRI-long_2_usage.html)

Charlene

chiangtw commented 7 months ago

Hi Charlene,

We used 1-base system in CircMiMi, i.e. "chr1:1000-2000" in your example.

Best, tw

algaebrown commented 7 months ago

Thanks! On Feb 15, 2024, 5:35 PM -0800, Tai-Wei Chiang @.***>, wrote:

Hi Charlene, We used 1-base system in CircMiMi, i.e. "chr1:1000-2000" in your example. Best, tw — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>