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Old 01-30-2011, 11:34 PM   #1
nazanin
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Location: vancouver

Join Date: Jan 2011
Posts: 3
Default ShortRead R package Aligned Read Output??

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) .

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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