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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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collect_circrnas.py script problem？ #17

Open WANGchuang715 opened 1 year ago

WANGchuang715 commented 1 year ago

I noticed that the command to extract intron in this script does not seem to be able to correctly generate the gtf file of intron. As shown in the figure below, the intron interval extracted from the test data provided by you is consistent with the gene interval. image 微信截图_20230726145813

egaffo commented 1 year ago

Thank you for reporting the issue. It is caused by the merged_exon.bed file that does not consider strandedness. I will release a fix.

WANGchuang715 commented 1 year ago

Thank you for reporting the issue. It is caused by the merged_exon.bed file that does not consider strandedness. I will release a fix.

The result of my test based on your modification still seems to be wrong.If you do not merge exon, the result seems to be correct. image