Using Gmap output

[hrajasim]

I am using the tool GMAP (Genomic Mapping and Alignment Program) for mRNA and EST Sequences developed by Thomas Wu and Colin Watanabe to map and align contigs identified by Abyss too from RNA-seq runs.

My goal is to now visualize the alignments for the 3 different samples against reference genome to fish for regions where there are differences in alignment (e.g., due to SNPs). How can I get there from the default output generated by Gmap tool (I also generated gmap alignments in PSL format)? Are there existing tools that can convert these formats to .bed format so that I can visualize them on UCSC genome browser or IGV?

I found WebGmap webservice but that only processes first 200 sequences from input FASTA - does not fit my needs.

Hope I can get some help on this forum.
Thanks,

[hrajasim]

Just figured that PSL format can be imported onto UCSC browser as a custom track. But I would still like to know what further down stream analysis tools can be applied on Gmap output.

[Jose Blanca]

I haven't used GMAP, can you generate bam files from it? There's a bunch of tools for the bam files to do this kind of analysis.