alignment using bowtie2
Hello everyone,
Just quick question on Alignment using in the current version of bowtie2.
I am doing alignment for the sequence read indicated below(30.fastq). However, getting the warning below.
Could not figure it out that does it mean? Is that mean I shall not give name for the out sam file?
bowtie2 --local -x bowtie 30.fastq –Sbowtie3.sam
Warning: Output file '–Sbowtie3.sam' was specified without -S. This will not work in future Bowtie 2 versions. Please use -S instead.
Then I thought this might be because I did not give space between -S and the the name bowtie3.sam
bowtie2 --local -x bowtie 30.fastq –S bowtie3.sam
but also got a Warning:
Output file '–S' was specified without -S. This will not work in future Bowtie 2 versions. Please use -S instead.
Extra parameter(s) specified: "bowtie3.sam"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/bin/bowtie2-align-s --wrapper basic-0 --local -x bowtie bowtie2.fastq –S bowtie3.sam
(ERR): bowtie2-align exited with value 1
Your help is apricated
thank you!
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