How to integrate Bowtie results into pipelines?

Prepare Bowtie Output

• Run Bowtie to generate alignment results. The typical output format is SAM (Sequence Alignment/Map).

 

• Ensure output files are properly named and stored in an organized directory within your pipeline workspace.

Convert SAM to BAM

• Use samtools view to convert SAM files to BAM format, as BAM files are more compressible and indexable.

 

• Execute the command: samtools view -bS input.sam > output.bam for conversion.

Sort BAM Files

• To facilitate faster access and analysis, sort the BAM files using samtools sort.

 

• Run the command: samtools sort output.bam -o sorted\_output.bam.

Index BAM Files

• Create an index for the sorted BAM files using samtools index to enable quick data retrieval.

 

• Execute: samtools index sorted\_output.bam.

Integrate into Pipeline

• Ensure your pipeline script uses updated references to the sorted and indexed BAM files for downstream analysis like variant calling or expression quantification.

 

• Use tools such as GATK, FreeBayes, or STAR, configuring them to utilize the sorted and indexed BAM files.

Cleanup and Maintenance

• Delete intermediate files like the initial SAM files if they are no longer needed, to save storage space.

 

• Maintain logs of each processing step for troubleshooting and validating the pipeline results.