Paired end FASTA to single BAM file

Question

[jyu429]

Hi,

I'm interested in taking two fastq files X_1.fq and X_2.fq creating a single bam file X.bam, unmapped to anything. Is there a way to do this with just bowtie2 and samtools? Thank you for the help!

[datascientist28]

Just curiously, what are reasons one would do this?

[igor]

I don't know about the original poster, but BAM is actually a more efficient file format. Check this post: http://blastedbio.blogspot.com/2011/10/fastq-must-die-long-live-sambam.html

Answer 1

[igor]

Would Picard be acceptable? You can do it easily with FastqToSam: https://broadinstitute.github.io/picard/command-line-overview.html#FastqToSam