SEQanswers - View Single Post - Visualing the alignment on a genome without annotations

NicoBxl · 04-12-2013, 01:16 AM

I you have a bam file from an aligner (you used bowtie, but you should use a splice-aware aligner like tophat or STAR) and a gtf (or gff) from cufflinks, you can use IGV to visualize the alignment and check the annotation created by cufflinks.

04-12-2013, 01:16 AM	#2
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	I you have a bam file from an aligner (you used bowtie, but you should use a splice-aware aligner like tophat or STAR) and a gtf (or gff) from cufflinks, you can use IGV to visualize the alignment and check the annotation created by cufflinks.