counting the unmapped reads

Question

[fi1d18]

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

[amirmhzadeh]

Your file is corrupt, my friend. As mentioned above, the command is fine.

[fi1d18]

Are you Iranian, Amir?

Answer 1

[Devon Ryan]

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

[fi1d18]

Devon,

He's just waiting for the result I can't report any error.

[Devon Ryan]

The file is corrupt, you can't give him a reliable result.

[fi1d18]

ok thank you

[atcg]

If you've downloaded the file from somewhere you can try downloading again.

Answer 2

[chemkhi.ali13]

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]