Distribution of multi mapped reads

Question

[biogrin]

Hi all, Can anyone please help me figure out how can I discover the number of times multi-mapped reads align more often? And with those results, how can I make a histogram with the distribution of multi-mapped reads? Thanks a lot

[Bastien Hervé]

Hello, you can try something like this :

samtools view -F 4 file.bam | awk '{printf $1"\n"}' | sort | uniq -cd

Get the reads mapped, take the read names, sort them, find and count the non unique ones. I let you try to plot your own histogram with these infos.

took it from here