Hi all,

I have a sam file, my supervisor asked me to count the number of unmapped reads, which command I should use?

samtools view -c -F 4 [file.sam] says that input is probably truncated

The command above would give you the number of mapped reads . if you want to get unmapped reads you should use "-f" not "-F"

samtools view -c -f 4 [file.sam]

Your command is fine, the file isn't. Ask your supervisor to double check that the file isn't corrupt.