Two Fastq Files And Alignment With Bwa.
1
1
Entering edit mode
9.4 years ago
KCC ★ 4.0k

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.)

bwa sam alignment fastq • 3.9k views
ADD COMMENT
9
Entering edit mode
9.4 years ago

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1688 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6