alignment using bowtie2

alignment using bowtie2

1

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!


bowtie2


sequencing


alignment

• 23 views

updated 35 minutes ago by

7.2k

written 2 hours ago by

▴

70

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


Login
before adding your answer.

Traffic: 3091 users visited in the last hour

Read more here: Source link