read.bowtie.tags: Read bowtie text alignment output file
In hms-dbmi/spp: ChIP-Seq Processing Pipeline

Reads in bowtie alignment results in text format

1	read.bowtie.tags(filename, read.tag.names = F, fix.chromosome.names = F)

`filename`	bowtie text output file
`read.tag.names`	Whether the tag names should be read in
`fix.chromosome.names`	Whether to remove ".fa" from the end of the sequence names

`tags`	A vector of 5' tag coordinates, with negative values corresponding to tags mapped to the negative strand.
`quality`	Number of mismatches
`names`	Tag names, if `read.tag.names` was set