Trying to check plasmid alignment

[chariko]

I have sequenced 2 samples (paired end). First sample is called Plas1 and second sample is called Micro_plas. I am interested in knowing whether Plas1 and Micro_plas are equal to another plasmid which I have the reference and view it in IGV. In order to do that I did the following:

1) Aligned Plas1 and Micro_plas to my plasmid reference (previously indexed) sequence for each paired end. (bwa)
2) Put together bot pair ends and create a unique sam file (bwa)
3) Transform sam to bam (samtools)
4) Filtered Plas1 and Micro_plas by quality (samtools)
5) Removed duplicates for both samples (picard)

Question 1: Sam files size for Plas1 is 20.1kb and 36.4Mb for Micro_plas. Taking this into account can I say only Micro_plas is equal to my reference and Plas1 no?

I tried viewing this in IGV but I was not able to see anything.

Question 2: I indexed my 5) bam files and loaded them into IGV (prior I loaded my reference plasmid as a genome). Nothing was observed in IGV. Did I did something wrong? Any clue?

Maybe if I calculate my coverage will it be enough?

[GenoMax]

Did you sort (and then index) your BAM files before trying to view them in IGV?

[chariko]

Thanks GenoMax for your answer, yes I sorted and then indexed but I still not see anything...