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How to run the BOWTIE short read aligner

This recipe demonstrates the use of the BOWTIE short read aligner to create a BAM file.

1 result • updated 4.5 years ago by Istvan Albert

This recipe demonstrates the use of the BOWTIE short read aligner to create a BAM file.

For more information see the

Bioinformatics Data Analysis online course.
Biostar Handbook for system setup and other information.

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# Stop on errors.
set -uex

# Reference genome accession number.
ACC=AF086833

# The SRR number for the sequencing data.
SRR=SRR1972739

# How many reads to unpack
N=10000

# The reference genome stored locally.
REF=refs/$ACC.fa

# The directory that store the reference.
mkdir -p refs

# Get the reference genome in FASTA format.
efetch -db nuccore -format fasta -id $ACC > $REF

# Build the bowtie2 index for the reference genome.
bowtie2-build $REF $REF  1>> log.txt 2>> log.txt

# Build IGV index for the reference genome.
samtools faidx $REF

# Obtain the FASTQ sequences for the SRR number.
fastq-dump -X $N --split-files $SRR  >> log.txt

# The name for the read pairs.
R1=${SRR}_1.fastq
R2=${SRR}_2.fastq

# Run the bowtie2 aligner. Creates a SAM file.
bowtie2 -x $REF -1 $R1 -2 $R2 > $SRR.sam 2>> log.txt

# Convert the SAM file to BAM format.
cat $SRR.sam | samtools sort > $SRR.bam

# Index the BAM file.
samtools index $SRR.bam

#Generate an alignment report.
samtools flagstat $SRR.bam > alignment-report.txt

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[ref]
label = "Accession number for the reference genome"
display = "TEXTBOX"
value = "AF086833"
help = "Must be an NCBI accession number"

[srr]
label = "SRA run number"
display = "TEXTBOX"
value = "SRR1972739"
help = "Must be an SRR run id number"

[settings]
id = 88
recipe_uid = "recipe-bowtie"
uid = "recipe-bowtie"
name = "How to run the BOWTIE short read aligner"
template = "How_to_run_the_BOWTIE_short_read_aligner_bio-data-analysis_88.sh"
image = "How_to_run_the_BOWTIE_short_read_aligner_bio-data-analysis_88.png"
project_uid = "bio-data-analysis"
url = "http://localhost8000"
help = "This recipe demonstrates the use of the BOWTIE short read aligner to create a BAM file.\n\nFor more information see the\n\n* [Bioinformatics Data Analysis][link]  online course.\n* [Biostar Handbook][book] for system setup and other information.\n\n[link]: https://www.biostarhandbook.com/edu/course/4/\n[book]: https://www.biostarhandbook.com/"

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