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YangLab / CIRCexplorer2

circular RNA analysis toolset
http://circexplorer2.readthedocs.org/
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Convert paired-end RNA-seq to single-read RNA-seq? #69

Open junjunlab opened 1 year ago

junjunlab commented 1 year ago

Hi, Thanks for this great tool. The CIRCexplorer2 align only supports single-end read data. The documentation mentioned It is recommended to convert paired-end RNA-seq to single-read RNA-seq before alignment. Can I zcat test1.fq.gz test2.fq.gz > test.fq.gz as input? Thanks!

best wished, JunZhang

kepbod commented 1 year ago

Yes, you could do this. If you want to use paired-end reads directly, I recommend you to use the STAR pipeline.

junjunlab commented 1 year ago

Hi, I want to use fast_circ.py annotate one command to run. But I got an error buitie2-build: unrecognized option '--threads'. I think the reason is that my python version is 2.7. CIRCexplorer2 can support python3 after version 2.3.0. But tophat2 only support python2.7 which means I could not use fast_circ.py annotate to run this pipeline in python2/3? Thanks!

best wished, JunZhang

kepbod commented 1 year ago

Could you offer the full information of errors?