Bowtie Paired End Alignment Question

[jpeace]

Hi All,
Does anyone know how bowtie pairs paired end reads for alignment? Does it simply pair the first read of the forward fastq file with the first read of reverse fastq file? Or does it pair them based on the x and y coordinates of the lane.

Essentially my question is if the reads are not ordered the same between the two files (or if some reads are removed from one file or the other) will bowtie still properly pair and align them? Thanks in advance!

[dpryan]

Pretty much every aligner requires the reads to be in the same order. Bowtie is no exception to that.

[mastal]

Bowtie assumes the reads are in the same order in the forward files and reverse files.

See the bowtie manual, under the section titled 'Command Line'.

http://bowtie-bio.sourceforge.net/manual.shtml

[jpeace]

Ok, that's what I needed to know. Thanks gents.