samtools idxstats

[Irina Pulyakhina]

Dear all,

With this command:

samtools idxstats aln.sorted.bam

You get a TAB delimited output where each line consists of ref.seq. name, ref.seq. length, number of mapped reads and number of unmapped reads. But the last line of this output is smth like this:

* 0 0 29000000

What does it mean? Does it mean that number of mapped reads in total (to any ref.seq.) is 29000000?

Thanks in advance,
Irina

[maubp]

The last line is unmapped reads (which are stored in SAM with a reference name of * if that helps to remember this).

[Irina Pulyakhina]

Thank you! Do you know whether I can get total number of mapped reads anyhow with samtools?

[av_d]

try samtools flagstat

[maubp]

Thank you! Do you know whether I can get total number of mapped reads anyhow with samtools?

Try my answer in this thread,

http://seqanswers.com/forums/showthread.php?p=53744#post53744