Tophat: Option --Bowtie Not A Unique Prefix

Question

[newDNASeqer]

This is a new problem for me: tophat: option --bowtie not a unique prefix, when I try to run tophat (ver 2.0.6) with bowtie 1.0.0 installed

tophat -p 4 --bowtie \ --fusion-search \ -z 0 \ --library-type fr-unstranded \ --GTF $GENOME.gtf --read-mismatches 3 \ --segment-mismatches 2 \ --segment-length 25 \ --bowtie-n \ -o outputFolder \ input_DIR/file1.fastq.gz

It's complaining tophat: option --bowtie not a unique prefix, I don't understand. Could someone help me? thanks

[Devon Ryan]

Do you mean --bowtie1 ? There is no plain --bowtie argument.

Answer 1

[jeales]

You need to specify --bowtie1 not --bowtie