I created a de novo transcriptome assembly using Trinity. I used Trinity's align_and_estimate_abundance.pl to align my reads using bowtie. I now want to visualize my reads and I have heard a lot about using IGV, however, do I need to sort and index my bowtie.bam file before loading it into IGV?
I tried samtools sort bowtie.bam and I am not sure what is supposed to happen to my .bam file but
If anyone can shed some light on this that would be much appreciated, Thank you, Nikelle