Recipe View

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 3.5 years ago by Istvan Albert

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

Steps demonstrated in the recipe:

Connecting to NCBI to download the Ebola reference genome.
Connecting to the Short Read Archive to download high throughput sequencing data
Indexing the Ebola reference genome with bowtie2-build
Aligning the short reads to the Ebola genome with bowtie2 to produce a SAM file.
Converting and sorting the SAM file into the BAM format.
Generating statistics report on the resulting BAM file.

For more information see:

Biostar Handbook handbook
Applied Bioinformatics course

Copy recipe

You need write access to the project to edit.

# 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

You need write access to the original recipe to edit.

Click the buttons on the right to create new fields.

Add text field Add float field Add data field Add checkbox Add dropdown Add upload field Add integer field Add radio button

Name

Recipe display name

Identifier

Unique identifier for the recipe.

Image :

Optional image for the recipe ( 500px Maximum ).

Rank:

Used to order recipes (optional).

Insert Image

From the web

From your computer

Cancel

Back