Two Fastq Files And Alignment With Bwa.

Question

[KCC]

I have two fastq files. I want to use bwa to produce two sam files as this is more efficent for me than merging the fastq files and running bwa on the bigger file. If I run bwa separately on the fastq files and merge the sam files later, will the result be different? (I don't know if this is an important detail, but I know a priori that the fastq files have reads from separate chromosomes.)

Answer 1

[Damian Kao]

Individual reads are mapped independently of each other. So mapping the reads in two chunks should produce the same mappings as a single file. However, I wouldn't expect mapping runs to always be identical as there is a random element to mapping repetitive hits.