alignment using bowtie2

Question

[adR]

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!

Answer 1

[Carlo Yague]

There are two issues in your code:

1. You miss the -1/-2/-U argument for the input fastq file
2. the "–S" you use is wrong (long dash). This is correct: "-S".

So the following code should work:

bowtie2 --local -x bowtie -U 30.fastq -S bowtie3.sam

[adR]

@Carlo Yague,

Thank you so much for your response! I am doing unpaired alignment for a single fastq. However what is U letter represent? Also Would you also type the code as you showed above for the paired-end alignment. Best Ad

[Carlo Yague]

-U means "unpaired", and is used for single-end fastq. If you have paired-end reads in two fastq files, you can use -1 read1.fastq -2 read2.fastq instead.