MR12072017
reczko@estia:/mnt/raid/data/results/fleming/dk$ samtools sort sortedKo01pos.bam.bam sortedKo01pos.sorted.bam
samtools sort sortedKo02pos.bam.bam sortedKo02pos.sorted.bam

samtools flagstat sortedKo01pos.sorted.bam
87478404 in total
0 QC failure
0 duplicates
87478404 mapped (100.00%)
87478404 paired in sequencing
43739202 read1
43739202 read2
83948534 properly paired (95.96%)
87478404 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
samtools flagstat sortedKo01pos.bam.bam  
87478404 in total
0 QC failure
0 duplicates
87478404 mapped (100.00%)
87478404 paired in sequencing
43739202 read1
43739202 read2
83948534 properly paired (95.96%)
87478404 with itself and mate mapped
0 singletons (0.00%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)


for i in *bam
do
 samtools index $i
 echo $i 
done

Dear Dimitris and Yiota,
I've copied the files Orsalia specified and prepared them for visualization in IGV
(sorted the alignments and added an .bai index file).
If you load the mm9 genome in IGV, you can add each bam file using
File -> Load from URL
and the following links:

http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedKO21pos.bam           
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedKO22pos.bam         
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedKOIFN1pos.bam  
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedKOIFN2pos.bam  
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedKo01pos.sorted.bam    
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedKo02pos.sorted.bam    
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedKo1IL4pos.bam         
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedKo2IL4pos.bam       
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedKo61pos.bam    
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedKo62pos.bam    
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedwt01IL4pos.bam 
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedwt01pos.bam.bam
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedwt02IL4pos.bam 
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedwt02pos.bam.bam
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedwt21pos.bam  
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedwt22pos.bam  
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedwt61pos.bam  
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedwt62pos.bam  
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedwtIFN1pos.bam
http://genomics-lab.fleming.gr/fleming/DKlab/orsalia/sortedwtIFN2pos.bam

BW,
Martin