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WGLab / UROBORUS

UROBORUS: circular RNA identification from RNA-Seq data
http://uroborus.openbioinformatics.org
MIT License
6 stars 11 forks source link

Is bowtie or bowtie2 being used? #3

Closed linatbeishan closed 8 years ago

linatbeishan commented 8 years ago

Hi, Kai. After reading the source code, I am kind of confused at the Bowtie software being used: is bowtie or bowtie2 being used? In tophat(v2.1.1), it will default choose bowtie2 unless you specify the --bowtie1 option; and in line 63 of your code, there is no such option specified, so I assume it's bowtie2, and provide the bowtie2 version of genome index to run by the -index option; But in line 96, you use the * bowtie* command, which isn't bowtie2 but with the same genome index provided through the -index option, and it failed to run; Could you kindly clarify this? Or you provided both the bowtie2 and bowtie genome index in the same path?

Thanks! linwei

xiaofengsong commented 8 years ago

Thanks linwei for pointing the bug, I have updated UROBORUS.pl. Pl use new version.

linatbeishan commented 8 years ago

Thanks, xiaofeng. so I think maybe you need to add the --bowtie1 option to the tophat run example in UROBORUS documentation as well: http://uroborus.openbioinformatics.org/en/latest/#reference

linwei