How to get information (Count) of Unique Mapped Reads to the Genome?

Question

[ramshahaya]

Hi,

I would like to check how many reads are uniquely aligned or mapped to the Genome (or Chromosomes)? I had aligned my data using the BWA aligner.

Would be grateful If I could get suggestions regarding this query.

I know that there is a command to check information about multi-mapped reads. If I am not mistaken.

samtools view -c fixed.bam

Thank you so much in advance.

[Michael]

samtools flagstats

[ramshahaya]

samtools flagstats fixed_Sort_Coordinate.bam

9307234 + 0 in total (QC-passed reads + QC-failed reads)

9256458 + 0 primary

50776 + 0 secondary

0 + 0 supplementary

0 + 0 duplicates

0 + 0 primary duplicates

9255274 + 0 mapped (99.44% : N/A)

9204498 + 0 primary mapped (99.44% : N/A)

9256458 + 0 paired in sequencing

4628229 + 0 read1

4628229 + 0 read2

9056900 + 0 properly paired (97.84% : N/A)

9164336 + 0 with itself and mate mapped

40162 + 0 singletons (0.43% : N/A)

79236 + 0 with mate mapped to a different chr

46085 + 0 with mate mapped to a different chr (mapQ>=5)

Thank you so much for the reply. Which row should I consider in the above results?

Is it possible to check how many uniquely mapped read on different chromosome? samtools idxstats will work? I know, samtools idxstats will provide information about mapped reads on the chromosome. If I am not mistaken. But I would like to see uniquely mapped read on a different chromosomes.

Thank you so much in advance.

[Michael]

Isn't it simply like that: unique = mapped - secondary?

Edit: Sorry, just consulted the documentation. Primary mapped should be a unique count.

primary mapped: 0x4, 0x100 and 0x800 bits not set

So the read is mapped (4 not set), and no secondary or other mapping exist and assuming BWA only gives a single alignment per read.

[ramshahaya]

Thanks a lot