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bioinfo-biols / CIRIquant

circular RNA quantification tools
https://sourceforge.net/projects/ciri/files/CIRIquant
MIT License
27 stars 18 forks source link

Add support for single end data and switch to python3 #71

Open nictru opened 1 month ago

nictru commented 1 month ago

Hello everyone,

First of all, thanks for the fantastic package. This PR contains the changes mentioned in the title. Both did not require a lot of code changes.

Updating to python3 allows using current versions of various dependencies. It also helps overcome some problems with bundling for bioconda (related PR).

Adding support for single-stranded datasets allows wider usage of the package. I understand that this needs to be thoroughly evaluated before it can make it into production.

If you are interested in adding these changes to the package, I am eager to contribute. If not, I will most likely keep maintaining a fork, as these functionalities are important for my use case.

Kevinzjy commented 1 month ago

Hi @nictru , thanks a lot for the helpful PR. There may be some concerns about the code for identifying single-ended / paired-ended BSJ reads. I will look into this, but maybe not very soon. Once done, I will be very happy to merge these codes into the next release.

nictru commented 1 month ago

Maybe I can perform an evaluation similar to the one in the paper on single-stranded data to increase confidence