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How to handle paired-end reads in Bowtie?

Learn how to handle paired-end reads in Bowtie. From preparing and quality checking to aligning and handling output, this guide covers all essential steps efficiently.

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How to handle paired-end reads in Bowtie?

 

Preparing Paired-End Reads

 

  • Obtain the paired-end FASTQ files from your sequencing provider. Typically these files will be labeled with suffixes such as `_R1` and `_R2` to indicate pair mates.
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  • Ensure quality control checks on the raw reads using tools like FASTQC to assess quality metrics and remove low-quality reads or adapter sequences.

 

Building an Index

 

  • Download your reference genome in FASTA format.
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  • Use Bowtie's `bowtie-build` command to create an index from the reference genome. The command will look like: `bowtie-build reference.fa index_prefix`. Replace `reference.fa` with your genome file and `index_prefix` with your chosen prefix for index files.

 

Aligning Paired-End Reads

 

  • Use the `bowtie` command to align the paired-end reads against the reference genome. A typical command might be: `bowtie -p 4 -x index_prefix -1 reads_R1.fastq -2 reads_R2.fastq -S output.sam`.
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  • Replace `index_prefix` with your index prefix, `reads_R1.fastq` and `reads_R2.fastq` with your paired-end FASTQ files, and `output.sam` with your desired output filename.
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  • Use the `-p` option to specify the number of processor cores to use, especially important if you're working on a multi-core system.

 

Handling Output

 

  • Inspect the output SAM file using samtools or another SAM/BAM viewer to ensure correct alignment.
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  • Convert SAM to BAM for storage efficiency: `samtools view -bS output.sam > output.bam`. If needed, sort the BAM file with `samtools sort output.bam -o sorted_output.bam` and index it with `samtools index sorted_output.bam` for visualization purposes.

 

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