|
By default, Tophat reports only "accepted_hits.sam". Is there any way to get a similar output with the unaligned reads ? Bowtie accepts the --un option to specify an output file, but Tophat does not recognize this option. Thanks for any input ! |
|
Simon Andrews in this thread (http://seqanswers.com/forums/showthread.php?t=6847) has a perl script that can use the original fastq and outputed sam files to find the unaligned reads. I've found no mention of a --un feature for Tophat. |
