Hello,

I input an aligned read file using readAligned() method in ShortRead
package:

file <- "42hr.bowtie"
aln <- readAligned(file, type = "Bowtie")

Then I do some modifications on the counts in the aln object, and want to
output the modified AlignedRead object, either in SAM format, or default
bowtie output format
(http://bowtie-bio.sourceforge.net/ma...-bowtie-output<http://bowtie-bio.sourceforge.net/manual.shtml#default-bowtie-output>)
.

So now the question is, how can I save the AlignedRead object to the disk in
either of the aforementioned formats?

Thanks!

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