How do I extract aligned reads from BAM file?

Question

[MAPK]

Hi, I have a fasta sequence to which I have aligned a fastq file using bowtie and got a BAM file. I need to extract all the reads in fastq file that aligned to my fasta sequence. Can I just extract all the reads from the BAM file I got from bowtie alignment in this case? Please suggest me if I should be doing something different. Thanks!

Answer 1

[Devon Ryan]

Yes, just use samtools fastq with the BAM file produced by bowtie2. You'll presumably want to use the -F 4 option.

[MAPK]

Thanks Devon. Since I will be extracting all the aligned reads from bam file, I had to use this command: samtools fasta input.bam -F 4 > output.fasta