Running an alignment with merged paired end reads, can I use bowtie2 or bwa mem?

Question

[m.radz]

I want to align some paired end reads that I merged and trimmed with BBmerge and BBduk to a referene genome. Bwa mem and bowtie2 seem to be popular options but I can't work out if merged paired end reads can be used as input for these programs. Has anyone done this? If not are there any other programs that can take merged paired end reads as input?

Answer 1

[ATpoint]

Sure, a merged PE read is simply a single-end read and both tools support that.

[m.radz]

For bowtie2 would I then flag the reads with -U (Comma-separated list of files containing unpaired reads to be aligned)? The only other options are -1,-2 for mate pairs and -interleaved

[ATpoint]

Yes, -U would be the choice.

[m.radz]

Thanks for your help!