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BenLangmead / bowtie

An ultrafast memory-efficient short read aligner
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Compatibility of Bowtie1 (v1.2.0 or later) with Tophat2 #138

Open rason81 opened 1 year ago

rason81 commented 1 year ago

bowtie1 with versions greater than 1.2.0 are not compatible with Tophat (v2.1.1), reporting things like "./SeqAn-1.4.2/seqan/basic/basic_exception.h:236 FAILED! (Uncaught exception of type St11logic_error: basic_string::_S_construct NULL not valid)". Possibly this issue is related to generation of *_genome.bwt.samheader.sam, because recent bowtie versions cannot generate sam headers with the empty input. Although there is alternative for Tophat, it is still at some point the optimal one. So, how to fix this issue?

yuanlizhanshi commented 3 months ago

i encountered the same problem, how did you slove this?