Using Bowtie2 for to align paired end reads

[sewellh]

Hi all,

Someone in our lab just got finished with sequencing and assembly of a number of contigs. The question was asked, whether or not she found HiSeq to be useful, or if we could use MiSeq in the future.

I thought if I could align the reads onto her contigs, then we could assess the coverage, and possibly whether or not HiSeq was necessary.

I found that Bowtie allows you to align short reads to a reference sequence.

I concatenated the FASTA files for all the contigs and successfully made a bowtie2 index from the file.

Now, I'm trying to map the paired-end reads onto the index:

./bowtie2 -S -p 2 DscP_kaster -1 KM01_GW1_TAAGGCGA_L005_R1_001.fastq -2 KM01_GW1_TAAGGCGA_L005_R2_001.fastq KM01_bowtie.sam

but keep coming up with the error

bowtie2-align exited with value 1

What am I doing wrong?

[dbrg77]

Try change the order of the option -S to the end, immediately before your sam file name, i.e.

do the following:

./bowtie2 -p 2 DscP_kaster -1 KM01_GW1_TAAGGCGA_L005_R1_001.fastq -2 KM01_GW1_TAAGGCGA_L005_R2_001.fastq -S KM01_bowtie.sam

[sewellh]

Hmm. I'm still getting the same error. Is there anything I can do to troubleshoot?

[cariboudoug]

I'm not sure, but do you need to add the "-x" flag indicating an index?

Gavin

[dpryan]

As Gavin suggested, you need to tell it what index to use:

bowtie2 -p 2 -x SOMEINDEX -1 KM01_GW1_TAAGGCGA_L005_R1_001.fastq -2 KM01_GW1_TAAGGCGA_L005_R2_001.fastq -S KM01_bowtie.sam

The index files themselves are built with bowtie2-build.

[sewellh]

That was the problem! Thank you! The tutorials I found said nothing about having the -x