Hi,
When using bwa-mem, is it necessary to use a different program for quality trimming prior to alignment? Since FASTX toolkit doesn't work with paired end reads I was thinking trimmomatic perhaps. But is this even necessary since bwa-mem has the -q flag for quality trimming?
And if I should use trimmomatic, how do I align the output with bwa-mem? Because as I understand it creates outputs for mapped reads and unmapped reads seperately.
Hope my question makes sense. I'm kinda new at this.
Thanks!
When using bwa-mem, is it necessary to use a different program for quality trimming prior to alignment? Since FASTX toolkit doesn't work with paired end reads I was thinking trimmomatic perhaps. But is this even necessary since bwa-mem has the -q flag for quality trimming?
And if I should use trimmomatic, how do I align the output with bwa-mem? Because as I understand it creates outputs for mapped reads and unmapped reads seperately.
Hope my question makes sense. I'm kinda new at this.
Thanks!
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