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egaffo / circompara2

Improved bioinformatic pipeline to identify and quantify circRNA expression from RNA-seq data by combining multiple circRNA detection methods
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why three different mappers ?? #9

Open hafizmtalha opened 2 years ago

hafizmtalha commented 2 years ago

circompara2 is using tophat, star and bowtie2. why all three? I mean is it necessary to run all three or One of them is enough ???

egaffo commented 2 years ago

It is not mandatory to use all mappers (actually, BWA and Segemehl are also run), you can select a different detection method combination. However, the current default combination was the best performing according to our tests. Check the circompara2 article for more details https://academic.oup.com/bib/article/23/1/bbab418/6409697

hafizmtalha commented 2 years ago

ok.. and what if I wanna skip 1 or 2 methods ?? where should I make a change ???

egaffo commented 2 years ago

You can set the CIRCRNA_METHODS parameter in the vars.py file. Check also here for more info about circompara2 options https://github.com/egaffo/circompara2#parameters