Hello. I have some .bam, bam.bai and .sam files corresponding to a Bioscope mapping of genome reads from SOLiD to a reference genome. I have had several issues even openig the files. As far as I a go I was able to open the alignment in Samtools, but not in IGV. I have to say that I am new at this so probably I am doing this wrong. When I try to open the .bam file in the graphic interface by clicking Tools>Run igvtools...>Count, etc, I got a .tdf null file and in the terminal I got these warnings:
Chromosome: gi|448814763|ref|NC_000962.3| not found in .genome file. Skipping. No features were found that matched chromosomes in genome...
What is happening here? How else can I visualize this alignment?
Thanks for the help.