bowtie error: extra parameters specified

[BioSlayer]

I am using bowtie to align short reads against a reference genome (hg19), I prepared the index of the chromosome in the ref genome and exported its location to a bin directory within bowtie as in

export HG_INDEX=/path_to_bowtie/bin/hg

so as to use it as

 $HG_INDEX

. Then I have the paired end short reads (about 50 bps) that I want to align and save in a sam format, so my command for running that is as follow

bowtie $HG_INDEX -q Combined.fastq -S  aligned.sam

and it generates an error as (Extra parameter(s) specified: "Combined.fastq", "aligned.sam")
So changing the command to :

bowtie $HG_INDEX -q Combined.fastq -S  --al aligned.sam

reduced the complaint to (Extra parameter(s) specified: "Combined.fastq")

I don't see any options in the bowtie switches that could enable me to avoid this error and searching around different websites looking for solution has proved futile and hence thought the SEQanswers is the best place to share this in hopes of finding a solution..


Thanks a lot

[rahilsethi]

Extra parameter(s) specified error

I too have been getting the same error
I am running bowtie version 0.12.7 for mapping SOLiD (colorspace 50bp read length) data
against human genome (hg19), on a linux platform (CentOS). When I run with the
following parameters:

$bowtie -C -f -Q sample_QV.qual -a --best --strata -n -l 20 --maxbts --chunkmbs 1000 -t --al 50_mapped_reads.csfasta --sam -p 5 /bowtie-ref-build/hg19/hg19 sample.csfasta 50_mapping.sam

it gives me the following error

Extra parameter(s) specified: "sample.csfasta", "50_mapping.sam"

and when I was running with default seed-length(-l) value by not defining
-l 20 i.e.:

$bowtie -C -f -Q sample_QV.qual -a --best --strata -n --maxbts --chunkmbs 1000 -t --al 50_mapped_reads.csfasta --sam -p 5 /bowtie-ref-build/hg19/hg19 sample.csfasta 50_mapping.sam

it runs successfully, generating the number of reads mapped and unmapped
details on the screen.

How can I then run the program at different seed length when I run bowtie
since, as seen above, it does not run whenever I mention seed length
within permissible range (i.e. 20 > 5 for read length 50bp)?