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Can't locate Bowtie2 index files

Hi,

I am trying to align my sequences to a reference genome but Bowtie2 is having trouble locating the index files that I downloaded from Illumina. I am working on a server and have read instructions about moving the files to the bowtie2 index subdirectory, however, this does not exist. It also says that bowtie2 is not a directory.

Does anyone know how I can solve this problem?

bowtie2 chip-seq alignment
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updated by flogin flogin • written by kdc15 • kdc15

Can you provide a link where you downloaded the sequence/annotation/index bundle from? Bundles from iGenomes contain indexes for multiple aligners. You don't need to move any files into directories etc as long as you provide right paths.

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written by GenoMax GenoMax

I am trying to align my sequences to a reference genome but Bowtie2 is having trouble locating the index files that I downloaded from Illumina

@Istvan has a simple guide on how you would use bowtie2 here.

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written by GenoMax GenoMax

Thank you, this helped!!

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written by kdc15 • kdc15

1 answer

To use the basic mapping function with bowtie2 you can do this: 

$ bowtie2-build reference_sequence.fasta reference_sequence.fasta.index
$ bowtie2 -x reference_sequence.fasta.index -U dataset_foward.fastq,dataset_reverse.fastq -S output.sam

Parameters: -x = input index, -U=fastq datasets separated by coma (e.g.case of paired-end datasets); -S= output in sam format.

If you want to visualize your mapping analysis on IGV or Artemis (e.g.), you need to use Samtools to convert sam in bam and create a sorted and index files:

$ samtools view -Sb output.sam -o output.bam
$ samtools sort output.bam -o output.sorted.bam
$ samtools index output.sorted.bam

I hope that it helps u.

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written by flogin flogin

Thank you, I have managed to do this now. Looks like I was using Bowtie1 instead of Bowtie2

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written by kdc15 • kdc15

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