forward and reverse reads with BWA

[jwhite]

Hi,

For those of you who use BWA:

Does BWA treat forward reads different from reverse reads?

The reason I ask is to determine whether the forward and reverse reads can be concatenated into a single file to supply to BWA.

Joe White

[dpryan]

By forward and reverse reads, are you referring to paired-end reads or reads which will map to the forward and reverse strand of the reference sequence? Presuming the former, don't concatenate them together. See, instead, the sampe command.

[jwhite]

By forward and reverse reads, are you referring to paired-end reads or reads which will map to the forward and reverse strand of the reference sequence? Presuming the former, don't concatenate them together. See, instead, the sampe command.

I was indeed referring to the former. A colleague is doing this, and I thought it unusual, so wanted to ask.

Thanks.
jw

[swbarnes2]

Concatenating them together is almost certainly the wrong thing to do.

For one thing, there is some unknown amount of sequence between the two ends of a paired end read. You might have some empirical data about what the likely size distribution of your library is, but that won't tell you how far apart any particular pair of reads is.