Hi all. Well, I've finally made my first post.
Here's my question. I have run Tophat using 27M 76nt Illumina reads mapped against a small (120kb) genome looking for spliced reads. The run appears to complete successfully and I have the typical output files such as junctions.bed which has 582 junctions.
However, I would really like to look at some of the spliced read alignments. Even when I use the command line option to save temp files I can't seem to find the reads that TopHat believes are spliced. I can see some fastq files but, of course, the read names have been changed. Is there a way to look at finer scale results such as this? Thanks for any help you can give.
Here's my question. I have run Tophat using 27M 76nt Illumina reads mapped against a small (120kb) genome looking for spliced reads. The run appears to complete successfully and I have the typical output files such as junctions.bed which has 582 junctions.
However, I would really like to look at some of the spliced read alignments. Even when I use the command line option to save temp files I can't seem to find the reads that TopHat believes are spliced. I can see some fastq files but, of course, the read names have been changed. Is there a way to look at finer scale results such as this? Thanks for any help you can give.
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