How do I extract aligned reads from BAM file?
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!
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Devon Ryan
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MAPK
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Yes, just use samtools fastq with the BAM file produced by bowtie2. You'll presumably want to use the -F 4 option.
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