How to visualize a set of sequence alignments that all have the same reference sequence?

Question

[nchuang]

I have a handful of similar sequences with a reference that I have aligned each one to with Needleman. As oppose to looking at each alignment one at a time, is it possible to view them all in relation to the reference since they all share the same reference? I'm hoping for it to look like a multiple sequence alignment essentially (I've tried doing MSA on this set but sequences with large indels do not align correctly).

Answer 1

[bharata1803]

Maybe you can use IGV application. In that application, you can load the reference and load all of your alignment fils in bam format. This is the example : https://www.dropbox.com/s/65podoee1sdvyzr/ENST00000309035.png?dl=0

[nchuang]

oh why didn't I think of that.thank you. What aligner would I use to generate global alignments in bam?

[bharata1803]

There are several tools for aligning and almost every aligner will produce bam. As for me, I use bowtie2 aligner. Bowtie website

[nchuang]

thank you

i ended up scripting something in python but using Needleman