Align reads with bowtie

Bowtie align reads on indexed genomes¶

Preliminary Note ¶

For the following steps, you will need 2 programs which an admin (with admin rights) has already installed - system-wide - for you, using the following command:

sudo apt update && apt install -y bowtie samtools

Prepare dmel_r6.54 bowtie index (Drosophila genome)¶

Bowtie indexing command line

bowtie-build --threads 6 dmel-all-chromosome-r6.54.fasta dmel.r6.54

This step should take about 2-3 min

Align the clipped fasta reads to dmel.r6.54 using `bowtie`¶

bowtie dmel.r6.54 -f clipped_GRH-103_R1.fasta \
                       -v 0 \
                       -k 1 \
                       -p 3 \
                       --al dmel_matched_GRH-103.fa \
                       --un unmatched_GRH-103.fa \
                       -S > GRH-103.sam

This step should take about 1 min

The bowtie alignment command explained

bowtie dmel.r6.54 -f clipped_GRH-103_R1.fasta # tells bowtie where is the index and the input clipped_GRH-103_R1.fasta
-v 0 -k 1 -p 3 # These are bowtie options
--al dmel_matched_GRH-103.fa # aligned reads will be in the dmel_matched_GRH-103.fa file
--un unmatched_GRH-103.fa # Unaligned reads will be in the unmatched_GRH-103.fa file
-S > GRH-103.sam # tells bowtie to return an alignement file in SAM format (-S) -S > GRH-103.sam

Convert SAM file to BAM file and sort the alignments by chromosome positions¶

samtools view -Sb -@ 3 GRH-103.sam | samtools sort -@ 3 -o GRH-103.bam

Check the result using

samtools view GRH-103.bam | more