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!
Just curiously, what are reasons one would do this?
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
Would Picard be acceptable? You can do it easily with FastqToSam: https://broadinstitute.github.io/picard/command-line-overview.html#FastqToSam