Viewing .Bam And .Bai Files In Igv

Question

[HNK]

Hey I have run tophat in galaxy server on sample, and i got deletion, insertion, junction and accepted_hits.bam files. Now i want to view the results of tophat in IGV. I know that for viewing tophat result (.nam file) in IGV i need to have .bam and .bai files. But i cannot figure out how to get this .bai file? Can you help me in figuring this out, so that i can view my result in IGV. And do i have to sort my bam file before viewing in IGV? Why do we need to sort this file and how should i do this sorting? I have less knowledg abou the command line tools, so can you kindly write the steps, how to do these tasks :)

Answer 1

[Sean Davis]

samtools index accepted_hits.bam

will generate the accepted_hits.bam.bai file.

[HNK]

thanks.. i just found in galaxy where bam file was created by tophat.. it also gives .bai files :) .. so i think i can download both files from there..