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I'm trying to execute
but I'm getting
This is quite annoying and I am sure there is some stupid syntax error on my part. Can you help spot it? This is bowtie version 1.0.
--EDIT: I reversed the place of the parameters:
and now it works. This is bizarre. Apparently, the sequence of the parameters makes a difference but it is not something I find obvious from the bowtie manual.
Code:
bowtie –m 1 -S /hts/galaxy/data/references/genomes/mus-musc/ens73/mm73 whole_sample.fastq whole_sample.sam
Code:
Extra parameter(s) specified: "whole_sample.fastq", "whole_sample.sam"
--EDIT: I reversed the place of the parameters:
Code:
bowtie -S -m 1 /hts/galaxy/data/references/genomes/mus-musc/ens73/mm73 whole_sample.fastq whole_sample.sam