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
so as to use it as
. 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
and it generates an error as (Extra parameter(s) specified: "Combined.fastq", "aligned.sam")
So changing the command to :
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
Code:
export HG_INDEX=/path_to_bowtie/bin/hg
Code:
$HG_INDEX
Code:
bowtie $HG_INDEX -q Combined.fastq -S aligned.sam
So changing the command to :
Code:
bowtie $HG_INDEX -q Combined.fastq -S --al aligned.sam
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
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